GSE_ID CONTACTPERSON SERIESTITLE SUMMARY CONTRIBUTORS EXPDESIGN PUBMEDID PAPER_ID SRA_STUDY_NUM TRACKNAME ASSAY STAGE TISSUE PUBLICATION GSM CAT_HIERARCHY STRAIN SPECIES_VERSION EXT_SPECIES_VERSION STATUS_LIST GSE_ROOT_FOLDER GSE_SPECIES_VER_ROOT_FOLDER GSE_BW_ROOT_FOLDER GSE_TPM_ROOT_FOLDER GSE_DE_ROOT_FOLDER GSE_PEAK_ROOT_FOLDER GSE_README_FILE 14025 Gert Jan Veenstra A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos Epigenetic mechanisms set apart the active and inactive regions in the genome of multicellular organisms to produce distinct cell fates during embryog Gert Jan Veenstra, Robert Akkers, Simon van Heeringen, Ulrike Jacobi, Eva Janssen-Megens, Kees-Jan Françoijs, Hendrik Stunnenberg, Gert Veenstra ChIP-seq profiles of two histone modifications (H3K4me3 and H3K27me3) and RNA Polymerase II, and a RNA-seq profile, of gastrula stage Xenopus tropicalis embryos 19758566 40368 SRP001343 WE - NF10-13 RNA-Seq NF10 embryo Akkers RC et al. (2009) GSM352204 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025/XENTR_10.0/RNA-Seq/Readme.txt 14025 Gert Jan Veenstra A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos Epigenetic mechanisms set apart the active and inactive regions in the genome of multicellular organisms to produce distinct cell fates during embryog Gert Jan Veenstra, Robert Akkers, Simon van Heeringen, Ulrike Jacobi, Eva Janssen-Megens, Kees-Jan Françoijs, Hendrik Stunnenberg, Gert Veenstra ChIP-seq profiles of two histone modifications (H3K4me3 and H3K27me3) and RNA Polymerase II, and a RNA-seq profile, of gastrula stage Xenopus tropicalis embryos 19758566 40368 SRP001343 H3K4me3 WE - NF11-12 ChIP-Seq NF11 embryo Akkers RC et al. (2009) GSM352202 ChIP-Seq/Epigenetic/H3K4me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025/XENTR_10.0/ChIP-Seq/Readme.txt 14025 Gert Jan Veenstra A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos Epigenetic mechanisms set apart the active and inactive regions in the genome of multicellular organisms to produce distinct cell fates during embryog Gert Jan Veenstra, Robert Akkers, Simon van Heeringen, Ulrike Jacobi, Eva Janssen-Megens, Kees-Jan Françoijs, Hendrik Stunnenberg, Gert Veenstra ChIP-seq profiles of two histone modifications (H3K4me3 and H3K27me3) and RNA Polymerase II, and a RNA-seq profile, of gastrula stage Xenopus tropicalis embryos 19758566 40368 SRP001343 Pol II WE - NF11-12 ChIP-Seq NF11 embryo Akkers RC et al. (2009) GSM419463 ChIP-Seq/Transcription Factor/Pol II tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025/XENTR_10.0/ChIP-Seq/Readme.txt 14025 Gert Jan Veenstra A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos Epigenetic mechanisms set apart the active and inactive regions in the genome of multicellular organisms to produce distinct cell fates during embryog Gert Jan Veenstra, Robert Akkers, Simon van Heeringen, Ulrike Jacobi, Eva Janssen-Megens, Kees-Jan Françoijs, Hendrik Stunnenberg, Gert Veenstra ChIP-seq profiles of two histone modifications (H3K4me3 and H3K27me3) and RNA Polymerase II, and a RNA-seq profile, of gastrula stage Xenopus tropicalis embryos 19758566 40368 SRP001343 H3K27me3 WE - NF11-12 ChIP-Seq NF11 embryo Akkers RC et al. (2009) GSM352203 ChIP-Seq/Epigenetic/H3K27me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14025/XENTR_10.0/ChIP-Seq/Readme.txt 14952 Mike Gilchrist High-throughput sequencing of small RNAs from Xenopus tropicalis High-throughput sequencing of small RNAs from Xenopus tropicalis (adult liver, adult skin, oocytes stage I, II, III, IV, V, VI).total RNA, ~18-42 nt Mike Gilchrist Illumina/Solexa sequencing of adult liver, adult skin, oocytes stage I, II, III, IV, V, VI 19628731 40115 SRP001036 oocyte - oocyte III-IV RNA-Seq oocyte III oocyte Armisen J et al. (2009) GSM372603 RNA-Seq/Embryonic Tissues/unfertilized egg tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/Readme.txt 14952 Mike Gilchrist High-throughput sequencing of small RNAs from Xenopus tropicalis High-throughput sequencing of small RNAs from Xenopus tropicalis (adult liver, adult skin, oocytes stage I, II, III, IV, V, VI).total RNA, ~18-42 nt Mike Gilchrist Illumina/Solexa sequencing of adult liver, adult skin, oocytes stage I, II, III, IV, V, VI 19628731 40115 SRP001036 liver - adult RNA-Seq adult liver Armisen J et al. (2009) GSM372598 RNA-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/Readme.txt 14952 Mike Gilchrist High-throughput sequencing of small RNAs from Xenopus tropicalis High-throughput sequencing of small RNAs from Xenopus tropicalis (adult liver, adult skin, oocytes stage I, II, III, IV, V, VI).total RNA, ~18-42 nt Mike Gilchrist Illumina/Solexa sequencing of adult liver, adult skin, oocytes stage I, II, III, IV, V, VI 19628731 40115 SRP001036 oocyte - oocyte I-II RNA-Seq oocyte I oocyte Armisen J et al. (2009) GSM372602 RNA-Seq/Embryonic Tissues/unfertilized egg tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/Readme.txt 14952 Mike Gilchrist High-throughput sequencing of small RNAs from Xenopus tropicalis High-throughput sequencing of small RNAs from Xenopus tropicalis (adult liver, adult skin, oocytes stage I, II, III, IV, V, VI).total RNA, ~18-42 nt Mike Gilchrist Illumina/Solexa sequencing of adult liver, adult skin, oocytes stage I, II, III, IV, V, VI 19628731 40115 SRP001036 oocyte - oocyte V-VI RNA-Seq oocyte V oocyte Armisen J et al. (2009) GSM372604 RNA-Seq/Embryonic Tissues/unfertilized egg tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/Readme.txt 14952 Mike Gilchrist High-throughput sequencing of small RNAs from Xenopus tropicalis High-throughput sequencing of small RNAs from Xenopus tropicalis (adult liver, adult skin, oocytes stage I, II, III, IV, V, VI).total RNA, ~18-42 nt Mike Gilchrist Illumina/Solexa sequencing of adult liver, adult skin, oocytes stage I, II, III, IV, V, VI 19628731 40115 SRP001036 skin - adult RNA-Seq adult skin Armisen J et al. (2009) GSM372601 RNA-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE14952/XENTR_10.0/RNA-Seq/Readme.txt 15556 Nelson Lau Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi Various small RNA libraries from purified microtubules or Xiwi immunoprecipitates or total extract from X.tropicalis or X.laevis egg extract. Variou Nelson Lau, Toshihiro Ohsumi, Mark Borowsky, Robert Kingston, Michael Blower Small RNAs were ligated with linkers and converted to cDNA by reverse transcription. cDNA library was amplified by PCR and was sequenced with either the 454 Genome Sequencer FLX platform or the Illumina GA-II platform. 19713941 40411 ooplasm - mature egg RNA-Seq mature egg ooplasm Lau NC et al. (2009) GSM389474 RNA-Seq/Embryonic Tissues/unfertilized egg laevis XL101 XENLA_10.1 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENLA_10.1/RNA-Seq/Readme.txt 15556 Nelson Lau Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi Various small RNA libraries from purified microtubules or Xiwi immunoprecipitates or total extract from X.tropicalis or X.laevis egg extract. Variou Nelson Lau, Toshihiro Ohsumi, Mark Borowsky, Robert Kingston, Michael Blower Small RNAs were ligated with linkers and converted to cDNA by reverse transcription. cDNA library was amplified by PCR and was sequenced with either the 454 Genome Sequencer FLX platform or the Illumina GA-II platform. 19713941 40411 egg - mature egg RNA-Seq mature egg egg Lau NC et al. (2009) GSM389477,GSM389478,GSM389479,GSM389480,GSM389481 RNA-Seq/Embryonic Tissues/unfertilized egg tropicalis XT100 XENTR_10.0 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENTR_10.0/RNA-Seq/Readme.txt 15556 Nelson Lau Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi Various small RNA libraries from purified microtubules or Xiwi immunoprecipitates or total extract from X.tropicalis or X.laevis egg extract. Variou Nelson Lau, Toshihiro Ohsumi, Mark Borowsky, Robert Kingston, Michael Blower Small RNAs were ligated with linkers and converted to cDNA by reverse transcription. cDNA library was amplified by PCR and was sequenced with either the 454 Genome Sequencer FLX platform or the Illumina GA-II platform. 19713941 40411 piwil1 ooplasm - mature egg RNA-Seq mature egg ooplasm Lau NC et al. (2009) GSM389473 RNA-Seq/Embryonic Tissues/unfertilized egg tropicalis XT100 XENTR_10.0 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENTR_10.0/RNA-Seq/Readme.txt 15556 Nelson Lau Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi Various small RNA libraries from purified microtubules or Xiwi immunoprecipitates or total extract from X.tropicalis or X.laevis egg extract. Variou Nelson Lau, Toshihiro Ohsumi, Mark Borowsky, Robert Kingston, Michael Blower Small RNAs were ligated with linkers and converted to cDNA by reverse transcription. cDNA library was amplified by PCR and was sequenced with either the 454 Genome Sequencer FLX platform or the Illumina GA-II platform. 19713941 40411 microtubule - mature egg RNA-Seq mature egg egg Lau NC et al. (2009) GSM389476 RNA-Seq/Embryonic Tissues/unfertilized egg laevis XL101 XENLA_10.1 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENLA_10.1/RNA-Seq/Readme.txt 15556 Nelson Lau Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi Various small RNA libraries from purified microtubules or Xiwi immunoprecipitates or total extract from X.tropicalis or X.laevis egg extract. Variou Nelson Lau, Toshihiro Ohsumi, Mark Borowsky, Robert Kingston, Michael Blower Small RNAs were ligated with linkers and converted to cDNA by reverse transcription. cDNA library was amplified by PCR and was sequenced with either the 454 Genome Sequencer FLX platform or the Illumina GA-II platform. 19713941 40411 microtubule - mature egg RNA-Seq mature egg egg Lau NC et al. (2009) GSM389464 RNA-Seq/Embryonic Tissues/unfertilized egg tropicalis XT100 XENTR_10.0 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENTR_10.0/RNA-Seq/Readme.txt 15556 Nelson Lau Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi Various small RNA libraries from purified microtubules or Xiwi immunoprecipitates or total extract from X.tropicalis or X.laevis egg extract. Variou Nelson Lau, Toshihiro Ohsumi, Mark Borowsky, Robert Kingston, Michael Blower Small RNAs were ligated with linkers and converted to cDNA by reverse transcription. cDNA library was amplified by PCR and was sequenced with either the 454 Genome Sequencer FLX platform or the Illumina GA-II platform. 19713941 40411 ooplasm - mature egg RNA-Seq mature egg ooplasm Lau NC et al. (2009) GSM389472 RNA-Seq/Embryonic Tissues/unfertilized egg tropicalis XT100 XENTR_10.0 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENTR_10.0/RNA-Seq/Readme.txt 15556 Nelson Lau Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi Various small RNA libraries from purified microtubules or Xiwi immunoprecipitates or total extract from X.tropicalis or X.laevis egg extract. Variou Nelson Lau, Toshihiro Ohsumi, Mark Borowsky, Robert Kingston, Michael Blower Small RNAs were ligated with linkers and converted to cDNA by reverse transcription. cDNA library was amplified by PCR and was sequenced with either the 454 Genome Sequencer FLX platform or the Illumina GA-II platform. 19713941 40411 piwil1 ooplasm - mature egg RNA-Seq mature egg ooplasm Lau NC et al. (2009) GSM389475 RNA-Seq/Embryonic Tissues/unfertilized egg laevis XL101 XENLA_10.1 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE15556/XENLA_10.1/RNA-Seq/Readme.txt 19173 Nicolas Robine Xenopus egg small RNA associated with Y12 antibody We examined in Xenopus tropicalis eggs piRNAs that are associated with Y12 antibody, which binds symmetrically methylated arginines that are present o Nicolas Robine, Nelson Lau, Eric Lai Sequencing of a cDNA library from small RNAs from the Y12 immunoprecipitate 20022248 40809 SRP001702 SNRPB egg - mature egg RNA-Seq mature egg egg Robine N et al. (2009) GSM475282 RNA-Seq/Embryonic Tissues/unfertilized egg tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE19173 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE19173/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE19173/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE19173/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE19173/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE19173/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE19173/XENTR_10.0/RNA-Seq/Readme.txt 21482 Gert Jan Veenstra Nucleotide composition-linked divergence of vertebrate core promoter architecture Transcription initiation involves the recruitment of basal transcription factors to the core promoter. A variety of core promoter elements exists, how Gert Jan Veenstra, Simon van Heeringen, Waseem Akhtar, Ulrike Jacobi, Robert Akkers, Yutaka Suzuki, Gert Veenstra ChIP-seq profiles of TBP in Xenopus tropicalis stage 12 embryos and TSS-seq profiles of Xenopus oocytes and stage 12 embryos 21284373 42761 SRP002372 WE - NF10-12 RNA-Seq NF10 embryo van Heeringen SJ et al. (2011) GSM632116 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE21482 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE21482/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE21482/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE21482/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE21482/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE21482/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE21482/XENTR_10.0/RNA-Seq/Readme.txt 21482 Gert Jan Veenstra Nucleotide composition-linked divergence of vertebrate core promoter architecture Transcription initiation involves the recruitment of basal transcription factors to the core promoter. A variety of core promoter elements exists, how Gert Jan Veenstra, Simon van Heeringen, Waseem Akhtar, Ulrike Jacobi, Robert Akkers, Yutaka Suzuki, Gert Veenstra ChIP-seq profiles of TBP in Xenopus tropicalis stage 12 embryos and TSS-seq profiles of Xenopus oocytes and stage 12 embryos 21284373 42761 SRP002372 TBP WE - NF12 ChIP-Seq NF12 embryo van Heeringen SJ et al. (2011) GSM537039 ChIP-Seq/Transcription Factor/TBP tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE21482 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE21482/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE21482/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE21482/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE21482/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE21482/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE21482/XENTR_10.0/ChIP-Seq/Readme.txt 21482 Gert Jan Veenstra Nucleotide composition-linked divergence of vertebrate core promoter architecture Transcription initiation involves the recruitment of basal transcription factors to the core promoter. A variety of core promoter elements exists, how Gert Jan Veenstra, Simon van Heeringen, Waseem Akhtar, Ulrike Jacobi, Robert Akkers, Yutaka Suzuki, Gert Veenstra ChIP-seq profiles of TBP in Xenopus tropicalis stage 12 embryos and TSS-seq profiles of Xenopus oocytes and stage 12 embryos 21284373 42761 SRP002372 WE - unfertilized egg RNA-Seq egg embryo van Heeringen SJ et al. (2011) GSM632117 RNA-Seq/Whole Embryo/unfertilized egg tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE21482 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE21482/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE21482/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE21482/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE21482/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE21482/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE21482/XENTR_10.0/RNA-Seq/Readme.txt 22146 Kevin Lebrigand microRNAs signatures of Xenopus laevis embryo epidermis at stage 11 (non ciliated) and 26 (ciliated) using high throughput sequencing Epidermis of Xenopus embryos forms a mucociliary epithelium constituted of basal, scattered, secreting and ciliated cells and is histologically simila Kevin Lebrigand, B Marcet, P Barbry, K Lebrigand 2 technical replicates of a pool of 50 explants for each stage 11.5 (non ciliated) and 26 (ciliated) of Xenopus laevis development 21602795 43315 SRP002578 WE - NF26 RNA-Seq NF26 embryo Marcet B et al. (2011) GSM550781,GSM550782 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE22146 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE22146/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE22146/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE22146/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE22146/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE22146/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE22146/XENLA_10.1/RNA-Seq/Readme.txt 22146 Kevin Lebrigand microRNAs signatures of Xenopus laevis embryo epidermis at stage 11 (non ciliated) and 26 (ciliated) using high throughput sequencing Epidermis of Xenopus embryos forms a mucociliary epithelium constituted of basal, scattered, secreting and ciliated cells and is histologically simila Kevin Lebrigand, B Marcet, P Barbry, K Lebrigand 2 technical replicates of a pool of 50 explants for each stage 11.5 (non ciliated) and 26 (ciliated) of Xenopus laevis development 21602795 43315 SRP002578 WE - NF11-11.5 RNA-Seq NF11 embryo Marcet B et al. (2011) GSM550779,GSM550780 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE22146 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE22146/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE22146/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE22146/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE22146/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE22146/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE22146/XENLA_10.1/RNA-Seq/Readme.txt 23913 Ozren Bogdanovic Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis DNA methylation is a tightly regulated epigenetic mark associated with transcriptional repression. Next-generation sequencing of purified methylated D Ozren Bogdanovic, Simon van Heeringen, Steven Long, Arjen Brinkman, Hendrik Stunnenberg, Peter Jones, Gert-Jan Veenstra MethylCap (methylated DNA affinity capture with the MBD domain of MeCP2), 500mM and 700mM elution fractions of stage 9 (blastula) and stage 12.5 (gastrula) Xenopus tropicalis DNA 21636662 43338 SRP003559 WE - NF12.5 MBD-Seq NF12.5 embryo Bogdanovic O et al. (2011) GSM589699 MBD-Seq/Epigenetic/ tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913/XENTR_10.0/MBD-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913/XENTR_10.0/MBD-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913/XENTR_10.0/MBD-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913/XENTR_10.0/MBD-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913/XENTR_10.0/MBD-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913/XENTR_10.0/MBD-Seq/Readme.txt 23913 Ozren Bogdanovic Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis DNA methylation is a tightly regulated epigenetic mark associated with transcriptional repression. Next-generation sequencing of purified methylated D Ozren Bogdanovic, Simon van Heeringen, Steven Long, Arjen Brinkman, Hendrik Stunnenberg, Peter Jones, Gert-Jan Veenstra MethylCap (methylated DNA affinity capture with the MBD domain of MeCP2), 500mM and 700mM elution fractions of stage 9 (blastula) and stage 12.5 (gastrula) Xenopus tropicalis DNA 21636662 43338 SRP003559 WE - NF9 MBD-Seq NF9 embryo Bogdanovic O et al. (2011) GSM589696 MBD-Seq/Epigenetic/ tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913/XENTR_10.0/MBD-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913/XENTR_10.0/MBD-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913/XENTR_10.0/MBD-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913/XENTR_10.0/MBD-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913/XENTR_10.0/MBD-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913/XENTR_10.0/MBD-Seq/Readme.txt 23913 Ozren Bogdanovic Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis DNA methylation is a tightly regulated epigenetic mark associated with transcriptional repression. Next-generation sequencing of purified methylated D Ozren Bogdanovic, Simon van Heeringen, Steven Long, Arjen Brinkman, Hendrik Stunnenberg, Peter Jones, Gert-Jan Veenstra MethylCap (methylated DNA affinity capture with the MBD domain of MeCP2), 500mM and 700mM elution fractions of stage 9 (blastula) and stage 12.5 (gastrula) Xenopus tropicalis DNA 21636662 43338 SRP003559 WE - NF9 MBD-Seq NF9 embryo Bogdanovic O et al. (2011) GSM589698 MBD-Seq/Epigenetic/ tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913/XENTR_10.0/MBD-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913/XENTR_10.0/MBD-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913/XENTR_10.0/MBD-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913/XENTR_10.0/MBD-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913/XENTR_10.0/MBD-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913/XENTR_10.0/MBD-Seq/Readme.txt 23913 Ozren Bogdanovic Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis DNA methylation is a tightly regulated epigenetic mark associated with transcriptional repression. Next-generation sequencing of purified methylated D Ozren Bogdanovic, Simon van Heeringen, Steven Long, Arjen Brinkman, Hendrik Stunnenberg, Peter Jones, Gert-Jan Veenstra MethylCap (methylated DNA affinity capture with the MBD domain of MeCP2), 500mM and 700mM elution fractions of stage 9 (blastula) and stage 12.5 (gastrula) Xenopus tropicalis DNA 21636662 43338 SRP003559 WE - NF12.5 MBD-Seq NF12.5 embryo Bogdanovic O et al. (2011) GSM589697 MBD-Seq/Epigenetic/ tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913/XENTR_10.0/MBD-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913/XENTR_10.0/MBD-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913/XENTR_10.0/MBD-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913/XENTR_10.0/MBD-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913/XENTR_10.0/MBD-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE23913/XENTR_10.0/MBD-Seq/Readme.txt 30067 Juan Larrain Deep sequencing of small RNAs in the Xenopus tropicalis gastrula Transposable elements comprise a large proportion of animal genomes. Transcripts of transposable elements are a source for the synthesis of endogenous Juan Larrain, Fernando Faunes, Natalia Sanchez, Mauricio Moreno, Gonzalo Olivares, Dasfne Lee-Liu, Leonardo Almonacid, Alex Slater, Tomas Norambuena, Ryan Taft, John Mattick, Francisco Melo Analysis of small RNAs expressed in the Xenopus tropicalis gastrula. 21818339 43632 SRP007217 dorsal WE - NF10 RNA-Seq NF10 dorsal Faunes F et al. (2011) GSM744253 RNA-Seq/Embryonic Tissues/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30067 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30067/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30067/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30067/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30067/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30067/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30067/XENTR_10.0/RNA-Seq/Readme.txt 30067 Juan Larrain Deep sequencing of small RNAs in the Xenopus tropicalis gastrula Transposable elements comprise a large proportion of animal genomes. Transcripts of transposable elements are a source for the synthesis of endogenous Juan Larrain, Fernando Faunes, Natalia Sanchez, Mauricio Moreno, Gonzalo Olivares, Dasfne Lee-Liu, Leonardo Almonacid, Alex Slater, Tomas Norambuena, Ryan Taft, John Mattick, Francisco Melo Analysis of small RNAs expressed in the Xenopus tropicalis gastrula. 21818339 43632 SRP007217 ventral WE - NF10 RNA-Seq NF10 embryo Faunes F et al. (2011) GSM744254 RNA-Seq/Embryonic Tissues/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30067 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30067/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30067/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30067/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30067/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30067/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30067/XENTR_10.0/RNA-Seq/Readme.txt 30146 Se-Jin Yoon HEB and E2A function as SMAD/FOXH1 cofactors Nodal signaling, mediated through SMAD transcription factors, is necessary for pluripotency maintenance and endoderm commitment. We have identified a Se-Jin Yoon, Andrea Wills, Edward Chuong, Rakhi Gupta, Julie Baker ChIP-seq of Smad2/3 and Input in X.tropicalis, stage 10.5 embryo. 21828274 43683 SRP007355 Smad2/3 WE - NF10.5 ChIP-Seq NF10.5 embryo Yoon SJ et al. (2011) GSM746611 ChIP-Seq/Transcription Factor/Smad2_3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30146 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30146/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30146/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30146/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30146/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30146/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30146/XENTR_10.0/ChIP-Seq/Readme.txt 30146 Se-Jin Yoon HEB and E2A function as SMAD/FOXH1 cofactors Nodal signaling, mediated through SMAD transcription factors, is necessary for pluripotency maintenance and endoderm commitment. We have identified a Se-Jin Yoon, Andrea Wills, Edward Chuong, Rakhi Gupta, Julie Baker ChIP-seq of Smad2/3 and Input in X.tropicalis, stage 10.5 embryo. 21828274 43683 SRP007355 input WE - NF10.5 ChIP-Seq NF10.5 embryo Yoon SJ et al. (2011) GSM746612 None tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30146 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30146/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30146/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30146/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30146/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30146/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE30146/XENTR_10.0/ChIP-Seq/Readme.txt 33444 Cei Abreu-Goodger miR-124 acts through coREST to control the onset of Sema3A sensitivity in navigating retinal growth cones During axon pathfinding, growth cones commonly exhibit changes in sensitivity to guidance cues that follow a strict timetable, even in the absence of Cei Abreu-Goodger, Marie-Laure Baudet, Krishna Zivraj, Alistair Muldal, Javier Armisen, Cherie Blenkiron, Leonard Goldstein, Erik Miska, Christine Holt Two independent experiments were performed. One with a single sample for each of 3 stages, and the second with 2 biological replicates of each stage. 22138647 44540 SRP009183 retina - NF24 RNA-Seq NF24 retina Baudet ML et al. (2011) GSM827025,GSM827026,GSM827027 RNA-Seq/Embryonic Tissues/Tailbud NF22 to NF44 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE33444 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE33444/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE33444/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE33444/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE33444/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE33444/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE33444/XENLA_10.1/RNA-Seq/Readme.txt 33444 Cei Abreu-Goodger miR-124 acts through coREST to control the onset of Sema3A sensitivity in navigating retinal growth cones During axon pathfinding, growth cones commonly exhibit changes in sensitivity to guidance cues that follow a strict timetable, even in the absence of Cei Abreu-Goodger, Marie-Laure Baudet, Krishna Zivraj, Alistair Muldal, Javier Armisen, Cherie Blenkiron, Leonard Goldstein, Erik Miska, Christine Holt Two independent experiments were performed. One with a single sample for each of 3 stages, and the second with 2 biological replicates of each stage. 22138647 44540 SRP009183 retina - NF40 RNA-Seq NF40 retina Baudet ML et al. (2011) GSM827031,GSM827032,GSM827033 RNA-Seq/Embryonic Tissues/Tailbud NF22 to NF44 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE33444 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE33444/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE33444/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE33444/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE33444/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE33444/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE33444/XENLA_10.1/RNA-Seq/Readme.txt 33444 Cei Abreu-Goodger miR-124 acts through coREST to control the onset of Sema3A sensitivity in navigating retinal growth cones During axon pathfinding, growth cones commonly exhibit changes in sensitivity to guidance cues that follow a strict timetable, even in the absence of Cei Abreu-Goodger, Marie-Laure Baudet, Krishna Zivraj, Alistair Muldal, Javier Armisen, Cherie Blenkiron, Leonard Goldstein, Erik Miska, Christine Holt Two independent experiments were performed. One with a single sample for each of 3 stages, and the second with 2 biological replicates of each stage. 22138647 44540 SRP009183 retina - NF32 RNA-Seq NF32 retina Baudet ML et al. (2011) GSM827028,GSM827029,GSM827030 RNA-Seq/Embryonic Tissues/Tailbud NF22 to NF44 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE33444 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE33444/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE33444/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE33444/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE33444/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE33444/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE33444/XENLA_10.1/RNA-Seq/Readme.txt 37452 Kin Fai Au RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. Kin Fai Au, Meng Tan, Kin Au, Arielle Yablonovitch, Andrea Wills, Julie Baker, Wing Wong, Jin Li Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole 22960373 45933 SRP012375 WE - NF31-32 RNA-Seq NF31 embryo Tan MH et al. (2013) GSM919934,GSM919956 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Readme.txt 37452 Kin Fai Au RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. Kin Fai Au, Meng Tan, Kin Au, Arielle Yablonovitch, Andrea Wills, Julie Baker, Wing Wong, Jin Li Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole 22960373 45933 SRP012375 WE - NF44-45 RNA-Seq NF44 embryo Tan MH et al. (2013) GSM919961 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Readme.txt 37452 Kin Fai Au RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. Kin Fai Au, Meng Tan, Kin Au, Arielle Yablonovitch, Andrea Wills, Julie Baker, Wing Wong, Jin Li Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole 22960373 45933 SRP012375 WE - NF19 RNA-Seq NF19 embryo Tan MH et al. (2013) GSM919928,GSM919929,GSM919950 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Readme.txt 37452 Kin Fai Au RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. Kin Fai Au, Meng Tan, Kin Au, Arielle Yablonovitch, Andrea Wills, Julie Baker, Wing Wong, Jin Li Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole 22960373 45933 SRP012375 WE - NF10 RNA-Seq NF10 embryo Tan MH et al. (2013) GSM919923,GSM919945 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Readme.txt 37452 Kin Fai Au RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. Kin Fai Au, Meng Tan, Kin Au, Arielle Yablonovitch, Andrea Wills, Julie Baker, Wing Wong, Jin Li Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole 22960373 45933 SRP012375 WE - NF15 RNA-Seq NF15 embryo Tan MH et al. (2013) GSM919926 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Readme.txt 37452 Kin Fai Au RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. Kin Fai Au, Meng Tan, Kin Au, Arielle Yablonovitch, Andrea Wills, Julie Baker, Wing Wong, Jin Li Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole 22960373 45933 SRP012375 WE - NF16-18 RNA-Seq NF16 embryo Tan MH et al. (2013) GSM919927,GSM919949 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Readme.txt 37452 Kin Fai Au RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. Kin Fai Au, Meng Tan, Kin Au, Arielle Yablonovitch, Andrea Wills, Julie Baker, Wing Wong, Jin Li Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole 22960373 45933 SRP012375 WE - NF2 RNA-Seq NF2 embryo Tan MH et al. (2013) GSM919938 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Readme.txt 37452 Kin Fai Au RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. Kin Fai Au, Meng Tan, Kin Au, Arielle Yablonovitch, Andrea Wills, Julie Baker, Wing Wong, Jin Li Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole 22960373 45933 SRP012375 WE - NF20-21 RNA-Seq NF20 embryo Tan MH et al. (2013) GSM919930,GSM919951 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Readme.txt 37452 Kin Fai Au RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. Kin Fai Au, Meng Tan, Kin Au, Arielle Yablonovitch, Andrea Wills, Julie Baker, Wing Wong, Jin Li Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole 22960373 45933 SRP012375 WE - NF22-23 RNA-Seq NF22 embryo Tan MH et al. (2013) GSM919931,GSM919952 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Readme.txt 37452 Kin Fai Au RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. Kin Fai Au, Meng Tan, Kin Au, Arielle Yablonovitch, Andrea Wills, Julie Baker, Wing Wong, Jin Li Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole 22960373 45933 SRP012375 WE - NF24-26 RNA-Seq NF24 embryo Tan MH et al. (2013) GSM919932,GSM919953,GSM919954 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Readme.txt 37452 Kin Fai Au RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. Kin Fai Au, Meng Tan, Kin Au, Arielle Yablonovitch, Andrea Wills, Julie Baker, Wing Wong, Jin Li Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole 22960373 45933 SRP012375 WE - NF3 RNA-Seq NF3 embryo Tan MH et al. (2013) GSM919939 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Readme.txt 37452 Kin Fai Au RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. Kin Fai Au, Meng Tan, Kin Au, Arielle Yablonovitch, Andrea Wills, Julie Baker, Wing Wong, Jin Li Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole 22960373 45933 SRP012375 WE - NF33/34 RNA-Seq NF33/34 embryo Tan MH et al. (2013) GSM919935,GSM919957 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Readme.txt 37452 Kin Fai Au RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. Kin Fai Au, Meng Tan, Kin Au, Arielle Yablonovitch, Andrea Wills, Julie Baker, Wing Wong, Jin Li Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole 22960373 45933 SRP012375 WE - NF37/38-39 RNA-Seq NF37/38 embryo Tan MH et al. (2013) GSM919958 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Readme.txt 37452 Kin Fai Au RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. Kin Fai Au, Meng Tan, Kin Au, Arielle Yablonovitch, Andrea Wills, Julie Baker, Wing Wong, Jin Li Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole 22960373 45933 SRP012375 WE - NF4 RNA-Seq NF4 embryo Tan MH et al. (2013) GSM919940 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Readme.txt 37452 Kin Fai Au RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. Kin Fai Au, Meng Tan, Kin Au, Arielle Yablonovitch, Andrea Wills, Julie Baker, Wing Wong, Jin Li Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole 22960373 45933 SRP012375 WE - NF40 RNA-Seq NF40 embryo Tan MH et al. (2013) GSM919936,GSM919959 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Readme.txt 37452 Kin Fai Au RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. Kin Fai Au, Meng Tan, Kin Au, Arielle Yablonovitch, Andrea Wills, Julie Baker, Wing Wong, Jin Li Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole 22960373 45933 SRP012375 WE - NF5 RNA-Seq NF5 embryo Tan MH et al. (2013) GSM919941 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Readme.txt 37452 Kin Fai Au RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. Kin Fai Au, Meng Tan, Kin Au, Arielle Yablonovitch, Andrea Wills, Julie Baker, Wing Wong, Jin Li Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole 22960373 45933 SRP012375 WE - NF6 RNA-Seq NF6 embryo Tan MH et al. (2013) GSM919942 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Readme.txt 37452 Kin Fai Au RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. Kin Fai Au, Meng Tan, Kin Au, Arielle Yablonovitch, Andrea Wills, Julie Baker, Wing Wong, Jin Li Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole 22960373 45933 SRP012375 WE - NF9 RNA-Seq NF9 embryo Tan MH et al. (2013) GSM919922,GSM919944 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Readme.txt 37452 Kin Fai Au RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. Kin Fai Au, Meng Tan, Kin Au, Arielle Yablonovitch, Andrea Wills, Julie Baker, Wing Wong, Jin Li Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole 22960373 45933 SRP012375 WE - NF11-12 RNA-Seq NF11 embryo Tan MH et al. (2013) GSM919924,GSM919925,GSM919946 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Readme.txt 37452 Kin Fai Au RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. Kin Fai Au, Meng Tan, Kin Au, Arielle Yablonovitch, Andrea Wills, Julie Baker, Wing Wong, Jin Li Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole 22960373 45933 SRP012375 WE - NF13-14 RNA-Seq NF13 embryo Tan MH et al. (2013) GSM919947,GSM919948 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Readme.txt 37452 Kin Fai Au RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. Kin Fai Au, Meng Tan, Kin Au, Arielle Yablonovitch, Andrea Wills, Julie Baker, Wing Wong, Jin Li Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole 22960373 45933 SRP012375 WE - NF41-42 RNA-Seq NF41 embryo Tan MH et al. (2013) GSM919937,GSM919960 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Readme.txt 37452 Kin Fai Au RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. Kin Fai Au, Meng Tan, Kin Au, Arielle Yablonovitch, Andrea Wills, Julie Baker, Wing Wong, Jin Li Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole 22960373 45933 SRP012375 WE - NF28 RNA-Seq NF28 embryo Tan MH et al. (2013) GSM919933,GSM919955 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Readme.txt 37452 Kin Fai Au RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. Kin Fai Au, Meng Tan, Kin Au, Arielle Yablonovitch, Andrea Wills, Julie Baker, Wing Wong, Jin Li Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole 22960373 45933 SRP012375 WE - NF8 RNA-Seq NF8 embryo Tan MH et al. (2013) GSM919943 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE37452/XENTR_10.0/RNA-Seq/Readme.txt 38605 Caroline Hill Genome-wide small RNA profiling and mRNA profiling of Xenopus embryos Here we report on genome-wide small RNA and transcriptome profiling of blastula, gastrula and neurula-stage Xenopus tropicalis embryos using deep sequ Caroline Hill, Joanne Harding, Stuart Horswell, Javier Armisen, Lyle Zimmerman, Eric Miska, Caroline Hill Examination of small RNAs and mRNA at 3 stages of Xenopus embryonic development. 24065776 47876 SRP013627 animal pole - NF10 RNA-Seq NF10 animal pole Harding JL et al. (2014) GSM946000 RNA-Seq/Embryonic Tissues/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/Readme.txt 38605 Caroline Hill Genome-wide small RNA profiling and mRNA profiling of Xenopus embryos Here we report on genome-wide small RNA and transcriptome profiling of blastula, gastrula and neurula-stage Xenopus tropicalis embryos using deep sequ Caroline Hill, Joanne Harding, Stuart Horswell, Javier Armisen, Lyle Zimmerman, Eric Miska, Caroline Hill Examination of small RNAs and mRNA at 3 stages of Xenopus embryonic development. 24065776 47876 SRP013627 WE - NF18 RNA-Seq NF18 embryo Harding JL et al. (2014) GSM946004 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/Readme.txt 38605 Caroline Hill Genome-wide small RNA profiling and mRNA profiling of Xenopus embryos Here we report on genome-wide small RNA and transcriptome profiling of blastula, gastrula and neurula-stage Xenopus tropicalis embryos using deep sequ Caroline Hill, Joanne Harding, Stuart Horswell, Javier Armisen, Lyle Zimmerman, Eric Miska, Caroline Hill Examination of small RNAs and mRNA at 3 stages of Xenopus embryonic development. 24065776 47876 SRP013627 WE - NF10 small RNA RNA-Seq NF10 embryo Harding JL et al. (2014) GSM945998 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/Readme.txt 38605 Caroline Hill Genome-wide small RNA profiling and mRNA profiling of Xenopus embryos Here we report on genome-wide small RNA and transcriptome profiling of blastula, gastrula and neurula-stage Xenopus tropicalis embryos using deep sequ Caroline Hill, Joanne Harding, Stuart Horswell, Javier Armisen, Lyle Zimmerman, Eric Miska, Caroline Hill Examination of small RNAs and mRNA at 3 stages of Xenopus embryonic development. 24065776 47876 SRP013627 WE - NF18 small RNA RNA-Seq NF18 embryo Harding JL et al. (2014) GSM945999 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/Readme.txt 38605 Caroline Hill Genome-wide small RNA profiling and mRNA profiling of Xenopus embryos Here we report on genome-wide small RNA and transcriptome profiling of blastula, gastrula and neurula-stage Xenopus tropicalis embryos using deep sequ Caroline Hill, Joanne Harding, Stuart Horswell, Javier Armisen, Lyle Zimmerman, Eric Miska, Caroline Hill Examination of small RNAs and mRNA at 3 stages of Xenopus embryonic development. 24065776 47876 SRP013627 WE - NF8 RNA-Seq NF8 embryo Harding JL et al. (2014) GSM946002 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/Readme.txt 38605 Caroline Hill Genome-wide small RNA profiling and mRNA profiling of Xenopus embryos Here we report on genome-wide small RNA and transcriptome profiling of blastula, gastrula and neurula-stage Xenopus tropicalis embryos using deep sequ Caroline Hill, Joanne Harding, Stuart Horswell, Javier Armisen, Lyle Zimmerman, Eric Miska, Caroline Hill Examination of small RNAs and mRNA at 3 stages of Xenopus embryonic development. 24065776 47876 SRP013627 WE - NF8 small RNA RNA-Seq NF8 embryo Harding JL et al. (2014) GSM945997 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/Readme.txt 38605 Caroline Hill Genome-wide small RNA profiling and mRNA profiling of Xenopus embryos Here we report on genome-wide small RNA and transcriptome profiling of blastula, gastrula and neurula-stage Xenopus tropicalis embryos using deep sequ Caroline Hill, Joanne Harding, Stuart Horswell, Javier Armisen, Lyle Zimmerman, Eric Miska, Caroline Hill Examination of small RNAs and mRNA at 3 stages of Xenopus embryonic development. 24065776 47876 SRP013627 vegetal pole - NF10 RNA-Seq NF10 vegetal pole Harding JL et al. (2014) GSM946001 RNA-Seq/Embryonic Tissues/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/Readme.txt 38605 Caroline Hill Genome-wide small RNA profiling and mRNA profiling of Xenopus embryos Here we report on genome-wide small RNA and transcriptome profiling of blastula, gastrula and neurula-stage Xenopus tropicalis embryos using deep sequ Caroline Hill, Joanne Harding, Stuart Horswell, Javier Armisen, Lyle Zimmerman, Eric Miska, Caroline Hill Examination of small RNAs and mRNA at 3 stages of Xenopus embryonic development. 24065776 47876 SRP013627 WE - NF10 RNA-Seq NF10 embryo Harding JL et al. (2014) GSM946003 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE38605/XENTR_10.0/RNA-Seq/Readme.txt 41161 Gert Jan Veenstra Principles of nucleation of H3K27 methylation during embryonic development During embryonic development, maintenance of cell identity and lineage commitment requires the Polycomb-group PRC2 complex, which catalyzes histone H3 Gert Jan Veenstra, Simon van Heeringen, Robert Akkers, Ila van Kruijsbergen, Lars Hanssen, Nilofar Sharifi, Gert-Jan Veenstra, M. Asif Arif ChIP-seq profiles of three histone modifications (H3K4me3, H3K27me3 and H3K4me1) and RNA Polymerase II, EZH2 and Jarid2 of Xenopus tropicalis embryos during development 24336765 47807 SRP015902 H3K4me1 WE - NF9 ChIP-Seq NF9 embryo van Heeringen SJ et al. (2014) GSM1009603 ChIP-Seq/Epigenetic/H3K4me1 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Readme.txt 41161 Gert Jan Veenstra Principles of nucleation of H3K27 methylation during embryonic development During embryonic development, maintenance of cell identity and lineage commitment requires the Polycomb-group PRC2 complex, which catalyzes histone H3 Gert Jan Veenstra, Simon van Heeringen, Robert Akkers, Ila van Kruijsbergen, Lars Hanssen, Nilofar Sharifi, Gert-Jan Veenstra, M. Asif Arif ChIP-seq profiles of three histone modifications (H3K4me3, H3K27me3 and H3K4me1) and RNA Polymerase II, EZH2 and Jarid2 of Xenopus tropicalis embryos during development 24336765 47807 SRP015902 Pol II WE - NF29/30 ChIP-Seq NF29/30 embryo van Heeringen SJ et al. (2014) GSM1009600 ChIP-Seq/Transcription Factor/Pol II tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Readme.txt 41161 Gert Jan Veenstra Principles of nucleation of H3K27 methylation during embryonic development During embryonic development, maintenance of cell identity and lineage commitment requires the Polycomb-group PRC2 complex, which catalyzes histone H3 Gert Jan Veenstra, Simon van Heeringen, Robert Akkers, Ila van Kruijsbergen, Lars Hanssen, Nilofar Sharifi, Gert-Jan Veenstra, M. Asif Arif ChIP-seq profiles of three histone modifications (H3K4me3, H3K27me3 and H3K4me1) and RNA Polymerase II, EZH2 and Jarid2 of Xenopus tropicalis embryos during development 24336765 47807 SRP015902 H3K27me3 WE - NF12 ChIP-Seq NF12 embryo van Heeringen SJ et al. (2014) GSM1009594 ChIP-Seq/Epigenetic/H3K27me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Readme.txt 41161 Gert Jan Veenstra Principles of nucleation of H3K27 methylation during embryonic development During embryonic development, maintenance of cell identity and lineage commitment requires the Polycomb-group PRC2 complex, which catalyzes histone H3 Gert Jan Veenstra, Simon van Heeringen, Robert Akkers, Ila van Kruijsbergen, Lars Hanssen, Nilofar Sharifi, Gert-Jan Veenstra, M. Asif Arif ChIP-seq profiles of three histone modifications (H3K4me3, H3K27me3 and H3K4me1) and RNA Polymerase II, EZH2 and Jarid2 of Xenopus tropicalis embryos during development 24336765 47807 SRP015902 H3K4me3 WE - NF12 ChIP-Seq NF12 embryo van Heeringen SJ et al. (2014) GSM1009590 ChIP-Seq/Epigenetic/H3K4me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Readme.txt 41161 Gert Jan Veenstra Principles of nucleation of H3K27 methylation during embryonic development During embryonic development, maintenance of cell identity and lineage commitment requires the Polycomb-group PRC2 complex, which catalyzes histone H3 Gert Jan Veenstra, Simon van Heeringen, Robert Akkers, Ila van Kruijsbergen, Lars Hanssen, Nilofar Sharifi, Gert-Jan Veenstra, M. Asif Arif ChIP-seq profiles of three histone modifications (H3K4me3, H3K27me3 and H3K4me1) and RNA Polymerase II, EZH2 and Jarid2 of Xenopus tropicalis embryos during development 24336765 47807 SRP015902 input WE - NF29/30 ChIP-Seq NF29/30 embryo van Heeringen SJ et al. (2014) GSM1009604 None tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Readme.txt 41161 Gert Jan Veenstra Principles of nucleation of H3K27 methylation during embryonic development During embryonic development, maintenance of cell identity and lineage commitment requires the Polycomb-group PRC2 complex, which catalyzes histone H3 Gert Jan Veenstra, Simon van Heeringen, Robert Akkers, Ila van Kruijsbergen, Lars Hanssen, Nilofar Sharifi, Gert-Jan Veenstra, M. Asif Arif ChIP-seq profiles of three histone modifications (H3K4me3, H3K27me3 and H3K4me1) and RNA Polymerase II, EZH2 and Jarid2 of Xenopus tropicalis embryos during development 24336765 47807 SRP015902 H3K27me3 WE - NF29/30 ChIP-Seq NF29/30 embryo van Heeringen SJ et al. (2014) GSM1009596 ChIP-Seq/Epigenetic/H3K27me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Readme.txt 41161 Gert Jan Veenstra Principles of nucleation of H3K27 methylation during embryonic development During embryonic development, maintenance of cell identity and lineage commitment requires the Polycomb-group PRC2 complex, which catalyzes histone H3 Gert Jan Veenstra, Simon van Heeringen, Robert Akkers, Ila van Kruijsbergen, Lars Hanssen, Nilofar Sharifi, Gert-Jan Veenstra, M. Asif Arif ChIP-seq profiles of three histone modifications (H3K4me3, H3K27me3 and H3K4me1) and RNA Polymerase II, EZH2 and Jarid2 of Xenopus tropicalis embryos during development 24336765 47807 SRP015902 H3K4me3 WE - NF29/30 ChIP-Seq NF29/30 embryo van Heeringen SJ et al. (2014) GSM1009592 ChIP-Seq/Epigenetic/H3K4me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Readme.txt 41161 Gert Jan Veenstra Principles of nucleation of H3K27 methylation during embryonic development During embryonic development, maintenance of cell identity and lineage commitment requires the Polycomb-group PRC2 complex, which catalyzes histone H3 Gert Jan Veenstra, Simon van Heeringen, Robert Akkers, Ila van Kruijsbergen, Lars Hanssen, Nilofar Sharifi, Gert-Jan Veenstra, M. Asif Arif ChIP-seq profiles of three histone modifications (H3K4me3, H3K27me3 and H3K4me1) and RNA Polymerase II, EZH2 and Jarid2 of Xenopus tropicalis embryos during development 24336765 47807 SRP015902 Ezh2 WE - NF9 ChIP-Seq NF9 embryo van Heeringen SJ et al. (2014) GSM1009601 ChIP-Seq/Transcription Factor/Ezh2 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Readme.txt 41161 Gert Jan Veenstra Principles of nucleation of H3K27 methylation during embryonic development During embryonic development, maintenance of cell identity and lineage commitment requires the Polycomb-group PRC2 complex, which catalyzes histone H3 Gert Jan Veenstra, Simon van Heeringen, Robert Akkers, Ila van Kruijsbergen, Lars Hanssen, Nilofar Sharifi, Gert-Jan Veenstra, M. Asif Arif ChIP-seq profiles of three histone modifications (H3K4me3, H3K27me3 and H3K4me1) and RNA Polymerase II, EZH2 and Jarid2 of Xenopus tropicalis embryos during development 24336765 47807 SRP015902 Pol II WE - NF9 ChIP-Seq NF9 embryo van Heeringen SJ et al. (2014) GSM1009597 ChIP-Seq/Transcription Factor/Pol II tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Readme.txt 41161 Gert Jan Veenstra Principles of nucleation of H3K27 methylation during embryonic development During embryonic development, maintenance of cell identity and lineage commitment requires the Polycomb-group PRC2 complex, which catalyzes histone H3 Gert Jan Veenstra, Simon van Heeringen, Robert Akkers, Ila van Kruijsbergen, Lars Hanssen, Nilofar Sharifi, Gert-Jan Veenstra, M. Asif Arif ChIP-seq profiles of three histone modifications (H3K4me3, H3K27me3 and H3K4me1) and RNA Polymerase II, EZH2 and Jarid2 of Xenopus tropicalis embryos during development 24336765 47807 SRP015902 H3K4me3 WE - NF9 ChIP-Seq NF9 embryo van Heeringen SJ et al. (2014) GSM1009589 ChIP-Seq/Epigenetic/H3K4me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Readme.txt 41161 Gert Jan Veenstra Principles of nucleation of H3K27 methylation during embryonic development During embryonic development, maintenance of cell identity and lineage commitment requires the Polycomb-group PRC2 complex, which catalyzes histone H3 Gert Jan Veenstra, Simon van Heeringen, Robert Akkers, Ila van Kruijsbergen, Lars Hanssen, Nilofar Sharifi, Gert-Jan Veenstra, M. Asif Arif ChIP-seq profiles of three histone modifications (H3K4me3, H3K27me3 and H3K4me1) and RNA Polymerase II, EZH2 and Jarid2 of Xenopus tropicalis embryos during development 24336765 47807 SRP015902 H3K27me3 WE - NF16 ChIP-Seq NF16 embryo van Heeringen SJ et al. (2014) GSM1009595 ChIP-Seq/Epigenetic/H3K27me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Readme.txt 41161 Gert Jan Veenstra Principles of nucleation of H3K27 methylation during embryonic development During embryonic development, maintenance of cell identity and lineage commitment requires the Polycomb-group PRC2 complex, which catalyzes histone H3 Gert Jan Veenstra, Simon van Heeringen, Robert Akkers, Ila van Kruijsbergen, Lars Hanssen, Nilofar Sharifi, Gert-Jan Veenstra, M. Asif Arif ChIP-seq profiles of three histone modifications (H3K4me3, H3K27me3 and H3K4me1) and RNA Polymerase II, EZH2 and Jarid2 of Xenopus tropicalis embryos during development 24336765 47807 SRP015902 H3K27me3 WE - NF9 ChIP-Seq NF9 embryo van Heeringen SJ et al. (2014) GSM1009593 ChIP-Seq/Epigenetic/H3K27me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Readme.txt 41161 Gert Jan Veenstra Principles of nucleation of H3K27 methylation during embryonic development During embryonic development, maintenance of cell identity and lineage commitment requires the Polycomb-group PRC2 complex, which catalyzes histone H3 Gert Jan Veenstra, Simon van Heeringen, Robert Akkers, Ila van Kruijsbergen, Lars Hanssen, Nilofar Sharifi, Gert-Jan Veenstra, M. Asif Arif ChIP-seq profiles of three histone modifications (H3K4me3, H3K27me3 and H3K4me1) and RNA Polymerase II, EZH2 and Jarid2 of Xenopus tropicalis embryos during development 24336765 47807 SRP015902 H3K4me3 WE - NF16 ChIP-Seq NF16 embryo van Heeringen SJ et al. (2014) GSM1009591 ChIP-Seq/Epigenetic/H3K4me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Readme.txt 41161 Gert Jan Veenstra Principles of nucleation of H3K27 methylation during embryonic development During embryonic development, maintenance of cell identity and lineage commitment requires the Polycomb-group PRC2 complex, which catalyzes histone H3 Gert Jan Veenstra, Simon van Heeringen, Robert Akkers, Ila van Kruijsbergen, Lars Hanssen, Nilofar Sharifi, Gert-Jan Veenstra, M. Asif Arif ChIP-seq profiles of three histone modifications (H3K4me3, H3K27me3 and H3K4me1) and RNA Polymerase II, EZH2 and Jarid2 of Xenopus tropicalis embryos during development 24336765 47807 SRP015902 Jarid2 WE - NF9 ChIP-Seq NF9 embryo van Heeringen SJ et al. (2014) GSM1009602 ChIP-Seq/Transcription Factor/Jarid2 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Readme.txt 41161 Gert Jan Veenstra Principles of nucleation of H3K27 methylation during embryonic development During embryonic development, maintenance of cell identity and lineage commitment requires the Polycomb-group PRC2 complex, which catalyzes histone H3 Gert Jan Veenstra, Simon van Heeringen, Robert Akkers, Ila van Kruijsbergen, Lars Hanssen, Nilofar Sharifi, Gert-Jan Veenstra, M. Asif Arif ChIP-seq profiles of three histone modifications (H3K4me3, H3K27me3 and H3K4me1) and RNA Polymerase II, EZH2 and Jarid2 of Xenopus tropicalis embryos during development 24336765 47807 SRP015902 Pol II WE - NF12 ChIP-Seq NF12 embryo van Heeringen SJ et al. (2014) GSM1009598 ChIP-Seq/Transcription Factor/Pol II tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Readme.txt 41161 Gert Jan Veenstra Principles of nucleation of H3K27 methylation during embryonic development During embryonic development, maintenance of cell identity and lineage commitment requires the Polycomb-group PRC2 complex, which catalyzes histone H3 Gert Jan Veenstra, Simon van Heeringen, Robert Akkers, Ila van Kruijsbergen, Lars Hanssen, Nilofar Sharifi, Gert-Jan Veenstra, M. Asif Arif ChIP-seq profiles of three histone modifications (H3K4me3, H3K27me3 and H3K4me1) and RNA Polymerase II, EZH2 and Jarid2 of Xenopus tropicalis embryos during development 24336765 47807 SRP015902 Pol II WE - NF16 ChIP-Seq NF16 embryo van Heeringen SJ et al. (2014) GSM1009599 ChIP-Seq/Transcription Factor/Pol II tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41161/XENTR_10.0/ChIP-Seq/Readme.txt 41338 Nuno Barbosa-Morais The evolutionary landscape of alternative splicing in vertebrate species How species with similar repertoires of protein coding genes differ so dramatically at the phenotypic level is poorly understood. From comparing the t Nuno Barbosa-Morais, Claudia Kutter, Stephen Watt, Duncan Odom, Benjamin Blencowe mRNA profiles of several organs (brain, liver, kidney, heart, skeletal muscle) in multiple vertebrate species (mouse, chicken, lizard, frog, pufferfish) generated by deep sequencing using Illumina HiSeq 23258890 46474 SRP015997 kidney - adult RNA-Seq adult kidney Barbosa-Morais NL et al. (2012) GSM1015167 RNA-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/Readme.txt 41338 Nuno Barbosa-Morais The evolutionary landscape of alternative splicing in vertebrate species How species with similar repertoires of protein coding genes differ so dramatically at the phenotypic level is poorly understood. From comparing the t Nuno Barbosa-Morais, Claudia Kutter, Stephen Watt, Duncan Odom, Benjamin Blencowe mRNA profiles of several organs (brain, liver, kidney, heart, skeletal muscle) in multiple vertebrate species (mouse, chicken, lizard, frog, pufferfish) generated by deep sequencing using Illumina HiSeq 23258890 46474 SRP015997 skeletal muscle - adult RNA-Seq adult skeletal muscle Barbosa-Morais NL et al. (2012) GSM1015169 RNA-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/Readme.txt 41338 Nuno Barbosa-Morais The evolutionary landscape of alternative splicing in vertebrate species How species with similar repertoires of protein coding genes differ so dramatically at the phenotypic level is poorly understood. From comparing the t Nuno Barbosa-Morais, Claudia Kutter, Stephen Watt, Duncan Odom, Benjamin Blencowe mRNA profiles of several organs (brain, liver, kidney, heart, skeletal muscle) in multiple vertebrate species (mouse, chicken, lizard, frog, pufferfish) generated by deep sequencing using Illumina HiSeq 23258890 46474 SRP015997 heart - adult RNA-Seq adult heart Barbosa-Morais NL et al. (2012) GSM1015168 RNA-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/Readme.txt 41338 Nuno Barbosa-Morais The evolutionary landscape of alternative splicing in vertebrate species How species with similar repertoires of protein coding genes differ so dramatically at the phenotypic level is poorly understood. From comparing the t Nuno Barbosa-Morais, Claudia Kutter, Stephen Watt, Duncan Odom, Benjamin Blencowe mRNA profiles of several organs (brain, liver, kidney, heart, skeletal muscle) in multiple vertebrate species (mouse, chicken, lizard, frog, pufferfish) generated by deep sequencing using Illumina HiSeq 23258890 46474 SRP015997 brain - adult RNA-Seq adult brain Barbosa-Morais NL et al. (2012) GSM1015165 RNA-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/Readme.txt 41338 Nuno Barbosa-Morais The evolutionary landscape of alternative splicing in vertebrate species How species with similar repertoires of protein coding genes differ so dramatically at the phenotypic level is poorly understood. From comparing the t Nuno Barbosa-Morais, Claudia Kutter, Stephen Watt, Duncan Odom, Benjamin Blencowe mRNA profiles of several organs (brain, liver, kidney, heart, skeletal muscle) in multiple vertebrate species (mouse, chicken, lizard, frog, pufferfish) generated by deep sequencing using Illumina HiSeq 23258890 46474 SRP015997 liver - adult RNA-Seq adult liver Barbosa-Morais NL et al. (2012) GSM1015166 RNA-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE41338/XENTR_10.0/RNA-Seq/Readme.txt 43512 David Sims Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates Two-thirds of gene promoters in mammals are associated with regions of non-methylated DNA, called CpG islands (CGIs), which counteract the repressive David Sims, Hannah Long, Chris Ponting, Robert Klose Bio-CAP was used to identify non-methylated regions of the genome in seven diverse vertebrates (human, mouse, platypus, chicken, lizard, frog and zebrafish) across a number of tissues. 23467541 46753 SRP017952 input testis - adult Bio-CAP-Seq adult testis Long HK et al. (2013) GSM1064690 Bio-CAP-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512/XENTR_10.0/Bio-CAP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512/XENTR_10.0/Bio-CAP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512/XENTR_10.0/Bio-CAP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512/XENTR_10.0/Bio-CAP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512/XENTR_10.0/Bio-CAP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512/XENTR_10.0/Bio-CAP-Seq/Readme.txt 43512 David Sims Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates Two-thirds of gene promoters in mammals are associated with regions of non-methylated DNA, called CpG islands (CGIs), which counteract the repressive David Sims, Hannah Long, Chris Ponting, Robert Klose Bio-CAP was used to identify non-methylated regions of the genome in seven diverse vertebrates (human, mouse, platypus, chicken, lizard, frog and zebrafish) across a number of tissues. 23467541 46753 SRP017952 testis - adult Bio-CAP-Seq adult testis Long HK et al. (2013) GSM1064691 Bio-CAP-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512/XENTR_10.0/Bio-CAP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512/XENTR_10.0/Bio-CAP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512/XENTR_10.0/Bio-CAP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512/XENTR_10.0/Bio-CAP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512/XENTR_10.0/Bio-CAP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512/XENTR_10.0/Bio-CAP-Seq/Readme.txt 43512 David Sims Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates Two-thirds of gene promoters in mammals are associated with regions of non-methylated DNA, called CpG islands (CGIs), which counteract the repressive David Sims, Hannah Long, Chris Ponting, Robert Klose Bio-CAP was used to identify non-methylated regions of the genome in seven diverse vertebrates (human, mouse, platypus, chicken, lizard, frog and zebrafish) across a number of tissues. 23467541 46753 SRP017952 WE - NF11-12 Bio-CAP-Seq NF11 embryo Long HK et al. (2013) GSM1064693 Bio-CAP-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512/XENTR_10.0/Bio-CAP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512/XENTR_10.0/Bio-CAP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512/XENTR_10.0/Bio-CAP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512/XENTR_10.0/Bio-CAP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512/XENTR_10.0/Bio-CAP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512/XENTR_10.0/Bio-CAP-Seq/Readme.txt 43512 David Sims Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates Two-thirds of gene promoters in mammals are associated with regions of non-methylated DNA, called CpG islands (CGIs), which counteract the repressive David Sims, Hannah Long, Chris Ponting, Robert Klose Bio-CAP was used to identify non-methylated regions of the genome in seven diverse vertebrates (human, mouse, platypus, chicken, lizard, frog and zebrafish) across a number of tissues. 23467541 46753 SRP017952 liver - adult Bio-CAP-Seq adult liver Long HK et al. (2013) GSM1064692 Bio-CAP-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512/XENTR_10.0/Bio-CAP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512/XENTR_10.0/Bio-CAP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512/XENTR_10.0/Bio-CAP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512/XENTR_10.0/Bio-CAP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512/XENTR_10.0/Bio-CAP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43512/XENTR_10.0/Bio-CAP-Seq/Readme.txt 43520 Anamaria Necsulea The evolution of lncRNA repertoires and expression patterns in tetrapods Only a minuscule fraction of long non-coding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into thei Anamaria Necsulea, Magali Soumillon, Angélica Liechti, Tasman Daish, Ulrich Zeller, Julie Baker, Frank Grutzner, Henrik Kaessmann, Maria Warnefors [Batch 1 and 2] To broaden our understanding of lncRNA evolution, we used an extensive RNA-seq dataset to establish lncRNA repertoires and homologous gene families in 11 tetrapod species. We analyzed the poly- adenylated transcriptomes of 8 organs (cortex/whole brain without cerebellum, cerebellum, heart, kidney, liver, placenta, ovary and testis) and 11 species (human, chimpanzee, bonobo, gorilla, orangutan, macaque, mouse, opossum, platypus, chicken and the frog Xenopus tropicalis), which shared a common ancestor ~370 millions of years (MY) ago. Our dataset included 47 strand-specific samples, which allowed us to confirm the orientation of gene predictions and to address the evolution of sense-antisense transcripts. See also GSE43721 (Soumillon et al, Cell Reports, 2013) for three strand-specific samples for mouse brain, liver and testis. 24463510 54076 SRP017959 kidney (male) - adult RNA-Seq adult kidney Necsulea A et al. (2014) GSM1064860 RNA-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/Readme.txt 43520 Anamaria Necsulea The evolution of lncRNA repertoires and expression patterns in tetrapods Only a minuscule fraction of long non-coding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into thei Anamaria Necsulea, Magali Soumillon, Angélica Liechti, Tasman Daish, Ulrich Zeller, Julie Baker, Frank Grutzner, Henrik Kaessmann, Maria Warnefors [Batch 1 and 2] To broaden our understanding of lncRNA evolution, we used an extensive RNA-seq dataset to establish lncRNA repertoires and homologous gene families in 11 tetrapod species. We analyzed the poly- adenylated transcriptomes of 8 organs (cortex/whole brain without cerebellum, cerebellum, heart, kidney, liver, placenta, ovary and testis) and 11 species (human, chimpanzee, bonobo, gorilla, orangutan, macaque, mouse, opossum, platypus, chicken and the frog Xenopus tropicalis), which shared a common ancestor ~370 millions of years (MY) ago. Our dataset included 47 strand-specific samples, which allowed us to confirm the orientation of gene predictions and to address the evolution of sense-antisense transcripts. See also GSE43721 (Soumillon et al, Cell Reports, 2013) for three strand-specific samples for mouse brain, liver and testis. 24463510 54076 SRP017959 ovary - adult RNA-Seq adult ovary Necsulea A et al. (2014) GSM1064865,GSM1196056 RNA-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/Readme.txt 43520 Anamaria Necsulea The evolution of lncRNA repertoires and expression patterns in tetrapods Only a minuscule fraction of long non-coding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into thei Anamaria Necsulea, Magali Soumillon, Angélica Liechti, Tasman Daish, Ulrich Zeller, Julie Baker, Frank Grutzner, Henrik Kaessmann, Maria Warnefors [Batch 1 and 2] To broaden our understanding of lncRNA evolution, we used an extensive RNA-seq dataset to establish lncRNA repertoires and homologous gene families in 11 tetrapod species. We analyzed the poly- adenylated transcriptomes of 8 organs (cortex/whole brain without cerebellum, cerebellum, heart, kidney, liver, placenta, ovary and testis) and 11 species (human, chimpanzee, bonobo, gorilla, orangutan, macaque, mouse, opossum, platypus, chicken and the frog Xenopus tropicalis), which shared a common ancestor ~370 millions of years (MY) ago. Our dataset included 47 strand-specific samples, which allowed us to confirm the orientation of gene predictions and to address the evolution of sense-antisense transcripts. See also GSE43721 (Soumillon et al, Cell Reports, 2013) for three strand-specific samples for mouse brain, liver and testis. 24463510 54076 SRP017959 heart (male) - adult RNA-Seq adult heart Necsulea A et al. (2014) GSM1064858 RNA-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/Readme.txt 43520 Anamaria Necsulea The evolution of lncRNA repertoires and expression patterns in tetrapods Only a minuscule fraction of long non-coding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into thei Anamaria Necsulea, Magali Soumillon, Angélica Liechti, Tasman Daish, Ulrich Zeller, Julie Baker, Frank Grutzner, Henrik Kaessmann, Maria Warnefors [Batch 1 and 2] To broaden our understanding of lncRNA evolution, we used an extensive RNA-seq dataset to establish lncRNA repertoires and homologous gene families in 11 tetrapod species. We analyzed the poly- adenylated transcriptomes of 8 organs (cortex/whole brain without cerebellum, cerebellum, heart, kidney, liver, placenta, ovary and testis) and 11 species (human, chimpanzee, bonobo, gorilla, orangutan, macaque, mouse, opossum, platypus, chicken and the frog Xenopus tropicalis), which shared a common ancestor ~370 millions of years (MY) ago. Our dataset included 47 strand-specific samples, which allowed us to confirm the orientation of gene predictions and to address the evolution of sense-antisense transcripts. See also GSE43721 (Soumillon et al, Cell Reports, 2013) for three strand-specific samples for mouse brain, liver and testis. 24463510 54076 SRP017959 brain (male) - adult RNA-Seq adult brain Necsulea A et al. (2014) GSM1064856 RNA-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/Readme.txt 43520 Anamaria Necsulea The evolution of lncRNA repertoires and expression patterns in tetrapods Only a minuscule fraction of long non-coding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into thei Anamaria Necsulea, Magali Soumillon, Angélica Liechti, Tasman Daish, Ulrich Zeller, Julie Baker, Frank Grutzner, Henrik Kaessmann, Maria Warnefors [Batch 1 and 2] To broaden our understanding of lncRNA evolution, we used an extensive RNA-seq dataset to establish lncRNA repertoires and homologous gene families in 11 tetrapod species. We analyzed the poly- adenylated transcriptomes of 8 organs (cortex/whole brain without cerebellum, cerebellum, heart, kidney, liver, placenta, ovary and testis) and 11 species (human, chimpanzee, bonobo, gorilla, orangutan, macaque, mouse, opossum, platypus, chicken and the frog Xenopus tropicalis), which shared a common ancestor ~370 millions of years (MY) ago. Our dataset included 47 strand-specific samples, which allowed us to confirm the orientation of gene predictions and to address the evolution of sense-antisense transcripts. See also GSE43721 (Soumillon et al, Cell Reports, 2013) for three strand-specific samples for mouse brain, liver and testis. 24463510 54076 SRP017959 brain (female) - adult RNA-Seq adult brain Necsulea A et al. (2014) GSM1064857 RNA-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/Readme.txt 43520 Anamaria Necsulea The evolution of lncRNA repertoires and expression patterns in tetrapods Only a minuscule fraction of long non-coding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into thei Anamaria Necsulea, Magali Soumillon, Angélica Liechti, Tasman Daish, Ulrich Zeller, Julie Baker, Frank Grutzner, Henrik Kaessmann, Maria Warnefors [Batch 1 and 2] To broaden our understanding of lncRNA evolution, we used an extensive RNA-seq dataset to establish lncRNA repertoires and homologous gene families in 11 tetrapod species. We analyzed the poly- adenylated transcriptomes of 8 organs (cortex/whole brain without cerebellum, cerebellum, heart, kidney, liver, placenta, ovary and testis) and 11 species (human, chimpanzee, bonobo, gorilla, orangutan, macaque, mouse, opossum, platypus, chicken and the frog Xenopus tropicalis), which shared a common ancestor ~370 millions of years (MY) ago. Our dataset included 47 strand-specific samples, which allowed us to confirm the orientation of gene predictions and to address the evolution of sense-antisense transcripts. See also GSE43721 (Soumillon et al, Cell Reports, 2013) for three strand-specific samples for mouse brain, liver and testis. 24463510 54076 SRP017959 heart (female) - adult RNA-Seq adult female organism Necsulea A et al. (2014) GSM1064859 RNA-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/Readme.txt 43520 Anamaria Necsulea The evolution of lncRNA repertoires and expression patterns in tetrapods Only a minuscule fraction of long non-coding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into thei Anamaria Necsulea, Magali Soumillon, Angélica Liechti, Tasman Daish, Ulrich Zeller, Julie Baker, Frank Grutzner, Henrik Kaessmann, Maria Warnefors [Batch 1 and 2] To broaden our understanding of lncRNA evolution, we used an extensive RNA-seq dataset to establish lncRNA repertoires and homologous gene families in 11 tetrapod species. We analyzed the poly- adenylated transcriptomes of 8 organs (cortex/whole brain without cerebellum, cerebellum, heart, kidney, liver, placenta, ovary and testis) and 11 species (human, chimpanzee, bonobo, gorilla, orangutan, macaque, mouse, opossum, platypus, chicken and the frog Xenopus tropicalis), which shared a common ancestor ~370 millions of years (MY) ago. Our dataset included 47 strand-specific samples, which allowed us to confirm the orientation of gene predictions and to address the evolution of sense-antisense transcripts. See also GSE43721 (Soumillon et al, Cell Reports, 2013) for three strand-specific samples for mouse brain, liver and testis. 24463510 54076 SRP017959 liver (female) - adult RNA-Seq adult female organism Necsulea A et al. (2014) GSM1064863 RNA-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/Readme.txt 43520 Anamaria Necsulea The evolution of lncRNA repertoires and expression patterns in tetrapods Only a minuscule fraction of long non-coding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into thei Anamaria Necsulea, Magali Soumillon, Angélica Liechti, Tasman Daish, Ulrich Zeller, Julie Baker, Frank Grutzner, Henrik Kaessmann, Maria Warnefors [Batch 1 and 2] To broaden our understanding of lncRNA evolution, we used an extensive RNA-seq dataset to establish lncRNA repertoires and homologous gene families in 11 tetrapod species. We analyzed the poly- adenylated transcriptomes of 8 organs (cortex/whole brain without cerebellum, cerebellum, heart, kidney, liver, placenta, ovary and testis) and 11 species (human, chimpanzee, bonobo, gorilla, orangutan, macaque, mouse, opossum, platypus, chicken and the frog Xenopus tropicalis), which shared a common ancestor ~370 millions of years (MY) ago. Our dataset included 47 strand-specific samples, which allowed us to confirm the orientation of gene predictions and to address the evolution of sense-antisense transcripts. See also GSE43721 (Soumillon et al, Cell Reports, 2013) for three strand-specific samples for mouse brain, liver and testis. 24463510 54076 SRP017959 liver (male) - adult RNA-Seq adult liver Necsulea A et al. (2014) GSM1064862 RNA-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/Readme.txt 43520 Anamaria Necsulea The evolution of lncRNA repertoires and expression patterns in tetrapods Only a minuscule fraction of long non-coding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into thei Anamaria Necsulea, Magali Soumillon, Angélica Liechti, Tasman Daish, Ulrich Zeller, Julie Baker, Frank Grutzner, Henrik Kaessmann, Maria Warnefors [Batch 1 and 2] To broaden our understanding of lncRNA evolution, we used an extensive RNA-seq dataset to establish lncRNA repertoires and homologous gene families in 11 tetrapod species. We analyzed the poly- adenylated transcriptomes of 8 organs (cortex/whole brain without cerebellum, cerebellum, heart, kidney, liver, placenta, ovary and testis) and 11 species (human, chimpanzee, bonobo, gorilla, orangutan, macaque, mouse, opossum, platypus, chicken and the frog Xenopus tropicalis), which shared a common ancestor ~370 millions of years (MY) ago. Our dataset included 47 strand-specific samples, which allowed us to confirm the orientation of gene predictions and to address the evolution of sense-antisense transcripts. See also GSE43721 (Soumillon et al, Cell Reports, 2013) for three strand-specific samples for mouse brain, liver and testis. 24463510 54076 SRP017959 testis - adult RNA-Seq adult testis Necsulea A et al. (2014) GSM1064864,GSM1196057 RNA-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/Readme.txt 43520 Anamaria Necsulea The evolution of lncRNA repertoires and expression patterns in tetrapods Only a minuscule fraction of long non-coding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into thei Anamaria Necsulea, Magali Soumillon, Angélica Liechti, Tasman Daish, Ulrich Zeller, Julie Baker, Frank Grutzner, Henrik Kaessmann, Maria Warnefors [Batch 1 and 2] To broaden our understanding of lncRNA evolution, we used an extensive RNA-seq dataset to establish lncRNA repertoires and homologous gene families in 11 tetrapod species. We analyzed the poly- adenylated transcriptomes of 8 organs (cortex/whole brain without cerebellum, cerebellum, heart, kidney, liver, placenta, ovary and testis) and 11 species (human, chimpanzee, bonobo, gorilla, orangutan, macaque, mouse, opossum, platypus, chicken and the frog Xenopus tropicalis), which shared a common ancestor ~370 millions of years (MY) ago. Our dataset included 47 strand-specific samples, which allowed us to confirm the orientation of gene predictions and to address the evolution of sense-antisense transcripts. See also GSE43721 (Soumillon et al, Cell Reports, 2013) for three strand-specific samples for mouse brain, liver and testis. 24463510 54076 SRP017959 kidney (female) - adult RNA-Seq adult female organism Necsulea A et al. (2014) GSM1064861 RNA-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43520/XENTR_10.0/RNA-Seq/Readme.txt 43652 Gert Jan Veenstra A Genome-Wide Survey of Maternal and Embryonic Transcripts during Xenopus tropicalis Development To analyze the dynamics and diversity of coding and non-coding transcripts during development, both polyadenylated mRNA and ribosomal RNA-depleted tot Gert Jan Veenstra, Sarita Paranjpe, Ulrike Jacobi, Simon van Heeringen, Gert Veenstra Profiles of polyadenylated mRNA (6 stages) and ribosomal RNA-depleted total RNA (3 stages) through early Xenopus tropicalis development 24195446 47572 SRP018091 oocyte - unfertilized egg RNA-Seq egg oocyte Paranjpe SS et al. (2013) GSM1067623 RNA-Seq/Embryonic Tissues/unfertilized egg tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/Readme.txt 43652 Gert Jan Veenstra A Genome-Wide Survey of Maternal and Embryonic Transcripts during Xenopus tropicalis Development To analyze the dynamics and diversity of coding and non-coding transcripts during development, both polyadenylated mRNA and ribosomal RNA-depleted tot Gert Jan Veenstra, Sarita Paranjpe, Ulrike Jacobi, Simon van Heeringen, Gert Veenstra Profiles of polyadenylated mRNA (6 stages) and ribosomal RNA-depleted total RNA (3 stages) through early Xenopus tropicalis development 24195446 47572 SRP018091 WE - NF16 RNA-Seq NF16 embryo Paranjpe SS et al. (2013) GSM1067627 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/Readme.txt 43652 Gert Jan Veenstra A Genome-Wide Survey of Maternal and Embryonic Transcripts during Xenopus tropicalis Development To analyze the dynamics and diversity of coding and non-coding transcripts during development, both polyadenylated mRNA and ribosomal RNA-depleted tot Gert Jan Veenstra, Sarita Paranjpe, Ulrike Jacobi, Simon van Heeringen, Gert Veenstra Profiles of polyadenylated mRNA (6 stages) and ribosomal RNA-depleted total RNA (3 stages) through early Xenopus tropicalis development 24195446 47572 SRP018091 WE - NF6 RNA-Seq NF6 embryo Paranjpe SS et al. (2013) GSM1067624 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/Readme.txt 43652 Gert Jan Veenstra A Genome-Wide Survey of Maternal and Embryonic Transcripts during Xenopus tropicalis Development To analyze the dynamics and diversity of coding and non-coding transcripts during development, both polyadenylated mRNA and ribosomal RNA-depleted tot Gert Jan Veenstra, Sarita Paranjpe, Ulrike Jacobi, Simon van Heeringen, Gert Veenstra Profiles of polyadenylated mRNA (6 stages) and ribosomal RNA-depleted total RNA (3 stages) through early Xenopus tropicalis development 24195446 47572 SRP018091 WE - NF12 RNA-Seq NF12 embryo Paranjpe SS et al. (2013) GSM1067626 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/Readme.txt 43652 Gert Jan Veenstra A Genome-Wide Survey of Maternal and Embryonic Transcripts during Xenopus tropicalis Development To analyze the dynamics and diversity of coding and non-coding transcripts during development, both polyadenylated mRNA and ribosomal RNA-depleted tot Gert Jan Veenstra, Sarita Paranjpe, Ulrike Jacobi, Simon van Heeringen, Gert Veenstra Profiles of polyadenylated mRNA (6 stages) and ribosomal RNA-depleted total RNA (3 stages) through early Xenopus tropicalis development 24195446 47572 SRP018091 WE - NF9 RNA-Seq NF9 embryo Paranjpe SS et al. (2013) GSM1067625 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/Readme.txt 43652 Gert Jan Veenstra A Genome-Wide Survey of Maternal and Embryonic Transcripts during Xenopus tropicalis Development To analyze the dynamics and diversity of coding and non-coding transcripts during development, both polyadenylated mRNA and ribosomal RNA-depleted tot Gert Jan Veenstra, Sarita Paranjpe, Ulrike Jacobi, Simon van Heeringen, Gert Veenstra Profiles of polyadenylated mRNA (6 stages) and ribosomal RNA-depleted total RNA (3 stages) through early Xenopus tropicalis development 24195446 47572 SRP018091 WE - NF29/30 RNA-Seq NF29/30 embryo Paranjpe SS et al. (2013) GSM1067628 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/Readme.txt 43652 Gert Jan Veenstra A Genome-Wide Survey of Maternal and Embryonic Transcripts during Xenopus tropicalis Development To analyze the dynamics and diversity of coding and non-coding transcripts during development, both polyadenylated mRNA and ribosomal RNA-depleted tot Gert Jan Veenstra, Sarita Paranjpe, Ulrike Jacobi, Simon van Heeringen, Gert Veenstra Profiles of polyadenylated mRNA (6 stages) and ribosomal RNA-depleted total RNA (3 stages) through early Xenopus tropicalis development 24195446 47572 SRP018091 WE - NF9 rd RNA-Seq NF9 embryo Paranjpe SS et al. (2013) GSM1067631 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/Readme.txt 43652 Gert Jan Veenstra A Genome-Wide Survey of Maternal and Embryonic Transcripts during Xenopus tropicalis Development To analyze the dynamics and diversity of coding and non-coding transcripts during development, both polyadenylated mRNA and ribosomal RNA-depleted tot Gert Jan Veenstra, Sarita Paranjpe, Ulrike Jacobi, Simon van Heeringen, Gert Veenstra Profiles of polyadenylated mRNA (6 stages) and ribosomal RNA-depleted total RNA (3 stages) through early Xenopus tropicalis development 24195446 47572 SRP018091 WE - NF6 rd RNA-Seq NF6 embryo Paranjpe SS et al. (2013) GSM1067630 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/Readme.txt 43652 Gert Jan Veenstra A Genome-Wide Survey of Maternal and Embryonic Transcripts during Xenopus tropicalis Development To analyze the dynamics and diversity of coding and non-coding transcripts during development, both polyadenylated mRNA and ribosomal RNA-depleted tot Gert Jan Veenstra, Sarita Paranjpe, Ulrike Jacobi, Simon van Heeringen, Gert Veenstra Profiles of polyadenylated mRNA (6 stages) and ribosomal RNA-depleted total RNA (3 stages) through early Xenopus tropicalis development 24195446 47572 SRP018091 oocyte - unfertilized egg rd RNA-Seq egg oocyte Paranjpe SS et al. (2013) GSM1067629 RNA-Seq/Embryonic Tissues/unfertilized egg tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE43652/XENTR_10.0/RNA-Seq/Readme.txt 45786 Panna Tandon Cardiac transcriptome of Tcf21-depleted Xenopus embryos The aim of the approach was to use RNAseq analysis to identify genes expressed in Xenopus epicardium that were affected by embryonic depletion of the Panna Tandon, Frank Conlon, Nirav Amin mRNA profiles of stage 44-45 Xenopus laevis sibling hearts from control or Tcf21-depleted embryos, were generated by deep sequencing using Illumina GAII. 23637334 47035 SRP020536 heart + tcf21 MO - NF44-45 RNA-Seq NF44 heart Tandon P et al. (2013) GSM1115089 Manipulations/Morpholino laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786/XENLA_10.1/RNA-Seq/Readme.txt 45786 Panna Tandon Cardiac transcriptome of Tcf21-depleted Xenopus embryos The aim of the approach was to use RNAseq analysis to identify genes expressed in Xenopus epicardium that were affected by embryonic depletion of the Panna Tandon, Frank Conlon, Nirav Amin mRNA profiles of stage 44-45 Xenopus laevis sibling hearts from control or Tcf21-depleted embryos, were generated by deep sequencing using Illumina GAII. 23637334 47035 SRP020536 heart + tcf21 MO - NF44-45 RNA-Seq NF44 heart Tandon P et al. (2013) GSM1115089 RNA-Seq/Embryonic Tissues/Tailbud NF22 to NF44 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786/XENLA_10.1/RNA-Seq/Readme.txt 45786 Panna Tandon Cardiac transcriptome of Tcf21-depleted Xenopus embryos The aim of the approach was to use RNAseq analysis to identify genes expressed in Xenopus epicardium that were affected by embryonic depletion of the Panna Tandon, Frank Conlon, Nirav Amin mRNA profiles of stage 44-45 Xenopus laevis sibling hearts from control or Tcf21-depleted embryos, were generated by deep sequencing using Illumina GAII. 23637334 47035 SRP020536 heart + tcf21 control MO - NF44-45 RNA-Seq NF44 heart Tandon P et al. (2013) GSM1115088 Manipulations/Morpholino laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786/XENLA_10.1/RNA-Seq/Readme.txt 45786 Panna Tandon Cardiac transcriptome of Tcf21-depleted Xenopus embryos The aim of the approach was to use RNAseq analysis to identify genes expressed in Xenopus epicardium that were affected by embryonic depletion of the Panna Tandon, Frank Conlon, Nirav Amin mRNA profiles of stage 44-45 Xenopus laevis sibling hearts from control or Tcf21-depleted embryos, were generated by deep sequencing using Illumina GAII. 23637334 47035 SRP020536 heart + tcf21 control MO - NF44-45 RNA-Seq NF44 heart Tandon P et al. (2013) GSM1115088 RNA-Seq/Embryonic Tissues/Tailbud NF22 to NF44 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE45786/XENLA_10.1/RNA-Seq/Readme.txt 48560 George Gentsch In vivo T-box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuro-mesodermal Bipotency. We defined genome-wide regulatory inputs of the T-box transcription factors Brachyury (Xbra), Eomesodermin (Eomes) and VegT that maintain neuro-mesode George Gentsch, George Gentsch, James Smith Binding profiles for Xbra, Eomes and VegT in X. tropicalis embryos (ChIP-Seq) 24055059 47416 SRP026570 input WE - NF20 ChIP-Seq NF20 embryo Gentsch GE et al. (2013) GSM1180941 None tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/Readme.txt 48560 George Gentsch In vivo T-box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuro-mesodermal Bipotency. We defined genome-wide regulatory inputs of the T-box transcription factors Brachyury (Xbra), Eomesodermin (Eomes) and VegT that maintain neuro-mesode George Gentsch, George Gentsch, James Smith Binding profiles for Xbra, Eomes and VegT in X. tropicalis embryos (ChIP-Seq) 24055059 47416 SRP026570 input WE - NF12.5 (vegt) ChIP-Seq NF12.5 embryo Gentsch GE et al. (2013) GSM1180937 None tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/Readme.txt 48560 George Gentsch In vivo T-box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuro-mesodermal Bipotency. We defined genome-wide regulatory inputs of the T-box transcription factors Brachyury (Xbra), Eomesodermin (Eomes) and VegT that maintain neuro-mesode George Gentsch, George Gentsch, James Smith Binding profiles for Xbra, Eomes and VegT in X. tropicalis embryos (ChIP-Seq) 24055059 47416 SRP026570 vegt WE - NF12.5 ChIP-Seq NF12.5 embryo Gentsch GE et al. (2013) GSM1180936 ChIP-Seq/Transcription Factor/vegt tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/Readme.txt 48560 George Gentsch In vivo T-box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuro-mesodermal Bipotency. We defined genome-wide regulatory inputs of the T-box transcription factors Brachyury (Xbra), Eomesodermin (Eomes) and VegT that maintain neuro-mesode George Gentsch, George Gentsch, James Smith Binding profiles for Xbra, Eomes and VegT in X. tropicalis embryos (ChIP-Seq) 24055059 47416 SRP026570 Eomes WE - NF12.5 ChIP-Seq NF12.5 embryo Gentsch GE et al. (2013) GSM1180934 ChIP-Seq/Transcription Factor/Eomes tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/Readme.txt 48560 George Gentsch In vivo T-box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuro-mesodermal Bipotency. We defined genome-wide regulatory inputs of the T-box transcription factors Brachyury (Xbra), Eomesodermin (Eomes) and VegT that maintain neuro-mesode George Gentsch, George Gentsch, James Smith Binding profiles for Xbra, Eomes and VegT in X. tropicalis embryos (ChIP-Seq) 24055059 47416 SRP026570 input WE - NF12.5 ChIP-Seq NF12.5 embryo Gentsch GE et al. (2013) GSM1180933,GSM1180939 None tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/Readme.txt 48560 George Gentsch In vivo T-box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuro-mesodermal Bipotency. We defined genome-wide regulatory inputs of the T-box transcription factors Brachyury (Xbra), Eomesodermin (Eomes) and VegT that maintain neuro-mesode George Gentsch, George Gentsch, James Smith Binding profiles for Xbra, Eomes and VegT in X. tropicalis embryos (ChIP-Seq) 24055059 47416 SRP026570 input WE - NF12.5 (xeomes) ChIP-Seq NF12.5 embryo Gentsch GE et al. (2013) GSM1180935 None tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/Readme.txt 48560 George Gentsch In vivo T-box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuro-mesodermal Bipotency. We defined genome-wide regulatory inputs of the T-box transcription factors Brachyury (Xbra), Eomesodermin (Eomes) and VegT that maintain neuro-mesode George Gentsch, George Gentsch, James Smith Binding profiles for Xbra, Eomes and VegT in X. tropicalis embryos (ChIP-Seq) 24055059 47416 SRP026570 Xbra WE - NF12.5 ChIP-Seq NF12.5 embryo Gentsch GE et al. (2013) GSM1180932,GSM1180938 ChIP-Seq/Transcription Factor/Xbra tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/Readme.txt 48560 George Gentsch In vivo T-box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuro-mesodermal Bipotency. We defined genome-wide regulatory inputs of the T-box transcription factors Brachyury (Xbra), Eomesodermin (Eomes) and VegT that maintain neuro-mesode George Gentsch, George Gentsch, James Smith Binding profiles for Xbra, Eomes and VegT in X. tropicalis embryos (ChIP-Seq) 24055059 47416 SRP026570 Xbra WE - NF20 ChIP-Seq NF20 embryo Gentsch GE et al. (2013) GSM1180940 ChIP-Seq/Transcription Factor/Xbra tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48560/XENTR_10.0/ChIP-Seq/Readme.txt 48663 George Gentsch In vivo T-box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuro-mesodermal Bipotency Brachyury (Xbra/Xbra3) knock-down embryos of the frog Xenopus tropicalis were profiled to quantify neuro-mesodermal cell fate switches at a transcript George Gentsch, George Gentsch, James Smith Transcriptional profiling of Xbra/Xbra3 double morphants at early tadpole stage (RNA-Seq) in biological triplicates. 24055059 47416 SRP026685 WE - NF20 RNA-Seq NF20 embryo Gentsch GE et al. (2013) GSM1183062 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/Readme.txt 48663 George Gentsch In vivo T-box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuro-mesodermal Bipotency Brachyury (Xbra/Xbra3) knock-down embryos of the frog Xenopus tropicalis were profiled to quantify neuro-mesodermal cell fate switches at a transcript George Gentsch, George Gentsch, James Smith Transcriptional profiling of Xbra/Xbra3 double morphants at early tadpole stage (RNA-Seq) in biological triplicates. 24055059 47416 SRP026685 WE + hbg1 MO - NF32 RNA-Seq NF32 embryo Gentsch GE et al. (2013) GSM1183059,GSM1183060,GSM1183061 Manipulations/Morpholino tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/Readme.txt 48663 George Gentsch In vivo T-box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuro-mesodermal Bipotency Brachyury (Xbra/Xbra3) knock-down embryos of the frog Xenopus tropicalis were profiled to quantify neuro-mesodermal cell fate switches at a transcript George Gentsch, George Gentsch, James Smith Transcriptional profiling of Xbra/Xbra3 double morphants at early tadpole stage (RNA-Seq) in biological triplicates. 24055059 47416 SRP026685 WE + hbg1 MO - NF32 RNA-Seq NF32 embryo Gentsch GE et al. (2013) GSM1183059,GSM1183060,GSM1183061 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/Readme.txt 48663 George Gentsch In vivo T-box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuro-mesodermal Bipotency Brachyury (Xbra/Xbra3) knock-down embryos of the frog Xenopus tropicalis were profiled to quantify neuro-mesodermal cell fate switches at a transcript George Gentsch, George Gentsch, James Smith Transcriptional profiling of Xbra/Xbra3 double morphants at early tadpole stage (RNA-Seq) in biological triplicates. 24055059 47416 SRP026685 WE + tbxt.2 MO + tbxt MO - NF32 RNA-Seq NF32 embryo Gentsch GE et al. (2013) GSM1183056,GSM1183057,GSM1183058 Manipulations/Morpholino tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/Readme.txt 48663 George Gentsch In vivo T-box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuro-mesodermal Bipotency Brachyury (Xbra/Xbra3) knock-down embryos of the frog Xenopus tropicalis were profiled to quantify neuro-mesodermal cell fate switches at a transcript George Gentsch, George Gentsch, James Smith Transcriptional profiling of Xbra/Xbra3 double morphants at early tadpole stage (RNA-Seq) in biological triplicates. 24055059 47416 SRP026685 WE + tbxt.2 MO + tbxt MO - NF32 RNA-Seq NF32 embryo Gentsch GE et al. (2013) GSM1183056,GSM1183057,GSM1183058 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE48663/XENTR_10.0/RNA-Seq/Readme.txt 50593 Taejoon Kwon Coordinated genomic control of ciliogenesis and cell movement by Rfx2 We have performed a systems-level analysis of the RFX/Daf-19 family transcription factor, Rfx2. Using a combination of high-throughput sequencing of R Taejoon Kwon, Mei-I Chung, Rakhi Gupta, Julie Baker, Edward Marcotte, John Wallingford RNA-seq: two biological replicates for control and RFX2 knockdown by morpholino injection, ChIP-seq: RFX2-GFP pulldown with GFP antibody, GFP only expression used as control 24424412 51735 SRP029582 input WE - NF20 ChIP-Seq NF20 embryo Chung MI et al. (2014) GSM1224377 None laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/ChIP-Seq/Readme.txt 50593 Taejoon Kwon Coordinated genomic control of ciliogenesis and cell movement by Rfx2 We have performed a systems-level analysis of the RFX/Daf-19 family transcription factor, Rfx2. Using a combination of high-throughput sequencing of R Taejoon Kwon, Mei-I Chung, Rakhi Gupta, Julie Baker, Edward Marcotte, John Wallingford RNA-seq: two biological replicates for control and RFX2 knockdown by morpholino injection, ChIP-seq: RFX2-GFP pulldown with GFP antibody, GFP only expression used as control 24424412 51735 SRP029582 rfx2 WE - NF20 ChIP-Seq NF20 embryo Chung MI et al. (2014) GSM1224376 ChIP-Seq/Transcription Factor/Rfx2 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/ChIP-Seq/Readme.txt 50593 Taejoon Kwon Coordinated genomic control of ciliogenesis and cell movement by Rfx2 We have performed a systems-level analysis of the RFX/Daf-19 family transcription factor, Rfx2. Using a combination of high-throughput sequencing of R Taejoon Kwon, Mei-I Chung, Rakhi Gupta, Julie Baker, Edward Marcotte, John Wallingford RNA-seq: two biological replicates for control and RFX2 knockdown by morpholino injection, ChIP-seq: RFX2-GFP pulldown with GFP antibody, GFP only expression used as control 24424412 51735 SRP029582 rfx2 WE - NF20 ChIP-Seq NF20 embryo Chung MI et al. (2014) GSM1224376 Manipulations/mRNA Injection laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/ChIP-Seq/Readme.txt 50593 Taejoon Kwon Coordinated genomic control of ciliogenesis and cell movement by Rfx2 We have performed a systems-level analysis of the RFX/Daf-19 family transcription factor, Rfx2. Using a combination of high-throughput sequencing of R Taejoon Kwon, Mei-I Chung, Rakhi Gupta, Julie Baker, Edward Marcotte, John Wallingford RNA-seq: two biological replicates for control and RFX2 knockdown by morpholino injection, ChIP-seq: RFX2-GFP pulldown with GFP antibody, GFP only expression used as control 24424412 51735 SRP029582 animal cap - NF20 RNA-Seq NF20 animal cap Chung MI et al. (2014) GSM1224372,GSM1224373 RNA-Seq/Embryonic Tissues/Neurula NF13 to NF21/animal cap laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/RNA-Seq/Readme.txt 50593 Taejoon Kwon Coordinated genomic control of ciliogenesis and cell movement by Rfx2 We have performed a systems-level analysis of the RFX/Daf-19 family transcription factor, Rfx2. Using a combination of high-throughput sequencing of R Taejoon Kwon, Mei-I Chung, Rakhi Gupta, Julie Baker, Edward Marcotte, John Wallingford RNA-seq: two biological replicates for control and RFX2 knockdown by morpholino injection, ChIP-seq: RFX2-GFP pulldown with GFP antibody, GFP only expression used as control 24424412 51735 SRP029582 animal cap + rfx2 MO - NF20 RNA-Seq NF20 animal cap Chung MI et al. (2014) GSM1224374,GSM1224375 Manipulations/Morpholino laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/RNA-Seq/Readme.txt 50593 Taejoon Kwon Coordinated genomic control of ciliogenesis and cell movement by Rfx2 We have performed a systems-level analysis of the RFX/Daf-19 family transcription factor, Rfx2. Using a combination of high-throughput sequencing of R Taejoon Kwon, Mei-I Chung, Rakhi Gupta, Julie Baker, Edward Marcotte, John Wallingford RNA-seq: two biological replicates for control and RFX2 knockdown by morpholino injection, ChIP-seq: RFX2-GFP pulldown with GFP antibody, GFP only expression used as control 24424412 51735 SRP029582 animal cap + rfx2 MO - NF20 RNA-Seq NF20 animal cap Chung MI et al. (2014) GSM1224374,GSM1224375 RNA-Seq/Embryonic Tissues/Neurula NF13 to NF21/animal cap laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE50593/XENLA_10.1/RNA-Seq/Readme.txt 52809 Stephen Eichhorn Poly(A)-tail profiling reveals an embryonic switch in translational control Poly(A) tails enhance the stability and translation of most eukaryotic messenger RNAs, but difficulties in globally measuring poly(A)-tail lengths hav Stephen Eichhorn, Alexander Subtelny, Stephen Eichhorn, Grace Chen, Hazel Sive, David Bartel 64 samples from a variety of species 24476825 48919 SRP033369 WE - NF9 RNA-Seq NF9 embryo Subtelny AO et al. (2014) GSM1276565 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/Readme.txt 52809 Stephen Eichhorn Poly(A)-tail profiling reveals an embryonic switch in translational control Poly(A) tails enhance the stability and translation of most eukaryotic messenger RNAs, but difficulties in globally measuring poly(A)-tail lengths hav Stephen Eichhorn, Alexander Subtelny, Stephen Eichhorn, Grace Chen, Hazel Sive, David Bartel 64 samples from a variety of species 24476825 48919 SRP033369 WE - NF3-4 RNA-Seq NF3 embryo Subtelny AO et al. (2014) GSM1276563 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/Readme.txt 52809 Stephen Eichhorn Poly(A)-tail profiling reveals an embryonic switch in translational control Poly(A) tails enhance the stability and translation of most eukaryotic messenger RNAs, but difficulties in globally measuring poly(A)-tail lengths hav Stephen Eichhorn, Alexander Subtelny, Stephen Eichhorn, Grace Chen, Hazel Sive, David Bartel 64 samples from a variety of species 24476825 48919 SRP033369 WE - NF12-12.5 RNA-Seq NF12 embryo Subtelny AO et al. (2014) GSM1316825 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/Readme.txt 52809 Stephen Eichhorn Poly(A)-tail profiling reveals an embryonic switch in translational control Poly(A) tails enhance the stability and translation of most eukaryotic messenger RNAs, but difficulties in globally measuring poly(A)-tail lengths hav Stephen Eichhorn, Alexander Subtelny, Stephen Eichhorn, Grace Chen, Hazel Sive, David Bartel 64 samples from a variety of species 24476825 48919 SRP033369 WE - NF3-4 (PAL-Seq) RNA-Seq NF3 embryo Subtelny AO et al. (2014) GSM1316823 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/Readme.txt 52809 Stephen Eichhorn Poly(A)-tail profiling reveals an embryonic switch in translational control Poly(A) tails enhance the stability and translation of most eukaryotic messenger RNAs, but difficulties in globally measuring poly(A)-tail lengths hav Stephen Eichhorn, Alexander Subtelny, Stephen Eichhorn, Grace Chen, Hazel Sive, David Bartel 64 samples from a variety of species 24476825 48919 SRP033369 WE - NF12-12.5 (PAL-Seq) RNA-Seq NF12 embryo Subtelny AO et al. (2014) GSM1316827 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/Readme.txt 52809 Stephen Eichhorn Poly(A)-tail profiling reveals an embryonic switch in translational control Poly(A) tails enhance the stability and translation of most eukaryotic messenger RNAs, but difficulties in globally measuring poly(A)-tail lengths hav Stephen Eichhorn, Alexander Subtelny, Stephen Eichhorn, Grace Chen, Hazel Sive, David Bartel 64 samples from a variety of species 24476825 48919 SRP033369 WE - NF9 (PAL-Seq) RNA-Seq NF9 embryo Subtelny AO et al. (2014) GSM1316824 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/Readme.txt 52809 Stephen Eichhorn Poly(A)-tail profiling reveals an embryonic switch in translational control Poly(A) tails enhance the stability and translation of most eukaryotic messenger RNAs, but difficulties in globally measuring poly(A)-tail lengths hav Stephen Eichhorn, Alexander Subtelny, Stephen Eichhorn, Grace Chen, Hazel Sive, David Bartel 64 samples from a variety of species 24476825 48919 SRP033369 WE - NF9 (Ribo-Seq) RNA-Seq NF9 embryo Subtelny AO et al. (2014) GSM1276566 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/Readme.txt 52809 Stephen Eichhorn Poly(A)-tail profiling reveals an embryonic switch in translational control Poly(A) tails enhance the stability and translation of most eukaryotic messenger RNAs, but difficulties in globally measuring poly(A)-tail lengths hav Stephen Eichhorn, Alexander Subtelny, Stephen Eichhorn, Grace Chen, Hazel Sive, David Bartel 64 samples from a variety of species 24476825 48919 SRP033369 WE - NF12-12.5 (Ribo-Seq) RNA-Seq NF12 embryo Subtelny AO et al. (2014) GSM1316826 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/Readme.txt 52809 Stephen Eichhorn Poly(A)-tail profiling reveals an embryonic switch in translational control Poly(A) tails enhance the stability and translation of most eukaryotic messenger RNAs, but difficulties in globally measuring poly(A)-tail lengths hav Stephen Eichhorn, Alexander Subtelny, Stephen Eichhorn, Grace Chen, Hazel Sive, David Bartel 64 samples from a variety of species 24476825 48919 SRP033369 WE - NF3-4 (Ribo-Seq) RNA-Seq NF3 embryo Subtelny AO et al. (2014) GSM1276564 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE52809/XENLA_10.1/RNA-Seq/Readme.txt 53652 William Chiu Genome-wide view of TGFb/Foxh1 regulation of the early mesendoderm program [ChIP-seq] We defined the genome-wide binding regions of Smad2/3 and Foxh1 at mid-gastrula stage Xenopus tropicalis embryos, at which Nodal signaling and Foxh1 a William Chiu, William Chiu, Ken Cho Binding profile of the TFs Smad2/3 and Foxh1 in gastrula stage (st10.5) Xenopus tropicalis embryos using ChIP-seq approach. 25359723 49634 SRP034730 Smad2/3 WE - NF10.5 ChIP-Seq NF10.5 embryo Chiu WT et al. (2014) GSM1298092,GSM1298093 ChIP-Seq/Transcription Factor/Smad2_3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53652 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53652/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53652/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53652/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53652/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53652/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53652/XENTR_10.0/ChIP-Seq/Readme.txt 53652 William Chiu Genome-wide view of TGFb/Foxh1 regulation of the early mesendoderm program [ChIP-seq] We defined the genome-wide binding regions of Smad2/3 and Foxh1 at mid-gastrula stage Xenopus tropicalis embryos, at which Nodal signaling and Foxh1 a William Chiu, William Chiu, Ken Cho Binding profile of the TFs Smad2/3 and Foxh1 in gastrula stage (st10.5) Xenopus tropicalis embryos using ChIP-seq approach. 25359723 49634 SRP034730 input WE - NF10.5 ChIP-Seq NF10.5 embryo Chiu WT et al. (2014) GSM1298094 None tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53652 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53652/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53652/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53652/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53652/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53652/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53652/XENTR_10.0/ChIP-Seq/Readme.txt 53652 William Chiu Genome-wide view of TGFb/Foxh1 regulation of the early mesendoderm program [ChIP-seq] We defined the genome-wide binding regions of Smad2/3 and Foxh1 at mid-gastrula stage Xenopus tropicalis embryos, at which Nodal signaling and Foxh1 a William Chiu, William Chiu, Ken Cho Binding profile of the TFs Smad2/3 and Foxh1 in gastrula stage (st10.5) Xenopus tropicalis embryos using ChIP-seq approach. 25359723 49634 SRP034730 Foxh1 WE - NF10.5 ChIP-Seq NF10.5 embryo Chiu WT et al. (2014) GSM1298090,GSM1298091 ChIP-Seq/Transcription Factor/Foxh1 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53652 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53652/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53652/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53652/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53652/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53652/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53652/XENTR_10.0/ChIP-Seq/Readme.txt 53653 William Chiu Genome-wide view of TGFb/Foxh1 regulation of the early mesendoderm program [RNA-seq] We identified Nodal and Foxh1 downstream targets by performing RNA-seq of embryos either treated with small molecule SB431542 or microinjected morphol William Chiu, William Chiu, Ken Cho Differential gene expression analyses of perturbed embryos (SB431542 treated, or Foxh1 MO injected) using RNA-seq 25359723 49634 SRP034731 WE + foxh1 MO - NF10.5 RNA-Seq NF10.5 embryo Chiu WT et al. (2014) GSM1298098 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/Readme.txt 53653 William Chiu Genome-wide view of TGFb/Foxh1 regulation of the early mesendoderm program [RNA-seq] We identified Nodal and Foxh1 downstream targets by performing RNA-seq of embryos either treated with small molecule SB431542 or microinjected morphol William Chiu, William Chiu, Ken Cho Differential gene expression analyses of perturbed embryos (SB431542 treated, or Foxh1 MO injected) using RNA-seq 25359723 49634 SRP034731 WE + foxh1 MO - NF10.5 RNA-Seq NF10.5 embryo Chiu WT et al. (2014) GSM1298098 Manipulations/Morpholino tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/Readme.txt 53653 William Chiu Genome-wide view of TGFb/Foxh1 regulation of the early mesendoderm program [RNA-seq] We identified Nodal and Foxh1 downstream targets by performing RNA-seq of embryos either treated with small molecule SB431542 or microinjected morphol William Chiu, William Chiu, Ken Cho Differential gene expression analyses of perturbed embryos (SB431542 treated, or Foxh1 MO injected) using RNA-seq 25359723 49634 SRP034731 WE + SB431542 - NF10.5 RNA-Seq NF10.5 embryo Chiu WT et al. (2014) GSM1298096 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/Readme.txt 53653 William Chiu Genome-wide view of TGFb/Foxh1 regulation of the early mesendoderm program [RNA-seq] We identified Nodal and Foxh1 downstream targets by performing RNA-seq of embryos either treated with small molecule SB431542 or microinjected morphol William Chiu, William Chiu, Ken Cho Differential gene expression analyses of perturbed embryos (SB431542 treated, or Foxh1 MO injected) using RNA-seq 25359723 49634 SRP034731 WE + SB431542 - NF10.5 RNA-Seq NF10.5 embryo Chiu WT et al. (2014) GSM1298096 Manipulations/Chemical tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/Readme.txt 53653 William Chiu Genome-wide view of TGFb/Foxh1 regulation of the early mesendoderm program [RNA-seq] We identified Nodal and Foxh1 downstream targets by performing RNA-seq of embryos either treated with small molecule SB431542 or microinjected morphol William Chiu, William Chiu, Ken Cho Differential gene expression analyses of perturbed embryos (SB431542 treated, or Foxh1 MO injected) using RNA-seq 25359723 49634 SRP034731 WE + EtOH - NF10.5 RNA-Seq NF10.5 embryo Chiu WT et al. (2014) GSM1298095 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/Readme.txt 53653 William Chiu Genome-wide view of TGFb/Foxh1 regulation of the early mesendoderm program [RNA-seq] We identified Nodal and Foxh1 downstream targets by performing RNA-seq of embryos either treated with small molecule SB431542 or microinjected morphol William Chiu, William Chiu, Ken Cho Differential gene expression analyses of perturbed embryos (SB431542 treated, or Foxh1 MO injected) using RNA-seq 25359723 49634 SRP034731 WE + EtOH - NF10.5 RNA-Seq NF10.5 embryo Chiu WT et al. (2014) GSM1298095 Manipulations/Chemical tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/Readme.txt 53653 William Chiu Genome-wide view of TGFb/Foxh1 regulation of the early mesendoderm program [RNA-seq] We identified Nodal and Foxh1 downstream targets by performing RNA-seq of embryos either treated with small molecule SB431542 or microinjected morphol William Chiu, William Chiu, Ken Cho Differential gene expression analyses of perturbed embryos (SB431542 treated, or Foxh1 MO injected) using RNA-seq 25359723 49634 SRP034731 WE - NF10.5 RNA-Seq NF10.5 embryo Chiu WT et al. (2014) GSM1298097 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE53653/XENTR_10.0/RNA-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 H3K27ac WE + SB431542 - NF9 ChIP-Seq NF9 embryo Gupta R et al. (2014) GSM1350520 ChIP-Seq/Epigenetic/H3K27ac tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 H3K27ac WE + SB431542 - NF9 ChIP-Seq NF9 embryo Gupta R et al. (2014) GSM1350520 Manipulations/Chemical tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 input WE - NF10.5 ChIP-Seq NF10.5 embryo Gupta R et al. (2014) GSM1350504 None tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 H3K4me1 WE - NF9 ChIP-Seq NF9 embryo Gupta R et al. (2014) GSM1350512 ChIP-Seq/Epigenetic/H3K4me1 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 H3K4me3 WE - NF10.5 ChIP-Seq NF10.5 embryo Gupta R et al. (2014) GSM1350510 ChIP-Seq/Epigenetic/H3K4me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 H3K27ac WE - NF8 ChIP-Seq NF8 embryo Gupta R et al. (2014) GSM1350514 ChIP-Seq/Epigenetic/H3K27ac tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 H3K4me1 WE - NF10.5 ChIP-Seq NF10.5 embryo Gupta R et al. (2014) GSM1350513 ChIP-Seq/Epigenetic/H3K4me1 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 WE + SB431542 - NF9 RNA-Seq NF9 embryo Gupta R et al. (2014) GSM1350525 Manipulations/Chemical tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 WE + SB431542 - NF9 RNA-Seq NF9 embryo Gupta R et al. (2014) GSM1350525 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 H3K4me3 WE - NF9 ChIP-Seq NF9 embryo Gupta R et al. (2014) GSM1350509 ChIP-Seq/Epigenetic/H3K4me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 H3K27me2me3 WE - NF8 ChIP-Seq NF8 embryo Gupta R et al. (2014) GSM1350517 ChIP-Seq/Epigenetic/H3K27me2me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 H3K27ac WE - NF10.5 ChIP-Seq NF10.5 embryo Gupta R et al. (2014) GSM1350516 ChIP-Seq/Epigenetic/H3K27ac tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 Smad2/3 WE - NF10.5 ChIP-Seq NF10.5 embryo Gupta R et al. (2014) GSM1350507 ChIP-Seq/Transcription Factor/Smad2_3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 H3K27me2me3 WE - NF10.5 ChIP-Seq NF10.5 embryo Gupta R et al. (2014) GSM1350519 ChIP-Seq/Epigenetic/H3K27me2me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 WE - NF10.5 RNA-Seq NF10.5 embryo Gupta R et al. (2014) GSM1350524 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 input WE - NF8 ChIP-Seq NF8 embryo Gupta R et al. (2014) GSM1350502 None tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 H3K4me3 WE - NF8 ChIP-Seq NF8 embryo Gupta R et al. (2014) GSM1350508 ChIP-Seq/Epigenetic/H3K4me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 Smad2/3 WE - NF8 ChIP-Seq NF8 embryo Gupta R et al. (2014) GSM1350505 ChIP-Seq/Transcription Factor/Smad2_3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 H3K4me1 WE - NF8 ChIP-Seq NF8 embryo Gupta R et al. (2014) GSM1350511 ChIP-Seq/Epigenetic/H3K4me1 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 input WE - NF9 ChIP-Seq NF9 embryo Gupta R et al. (2014) GSM1350503 None tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 H3K27ac WE - NF9 ChIP-Seq NF9 embryo Gupta R et al. (2014) GSM1350515 ChIP-Seq/Epigenetic/H3K27ac tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 Smad2/3 WE - NF9 ChIP-Seq NF9 embryo Gupta R et al. (2014) GSM1350506 ChIP-Seq/Transcription Factor/Smad2_3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 H3K27me2me3 WE - NF9 ChIP-Seq NF9 embryo Gupta R et al. (2014) GSM1350518 ChIP-Seq/Epigenetic/H3K27me2me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 H3K4me1 WE + SB431542 - NF9 ChIP-Seq NF9 embryo Gupta R et al. (2014) GSM1350521 ChIP-Seq/Epigenetic/H3K4me1 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 H3K4me1 WE + SB431542 - NF9 ChIP-Seq NF9 embryo Gupta R et al. (2014) GSM1350521 Manipulations/Chemical tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/ChIP-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 WE - NF9 RNA-Seq NF9 embryo Gupta R et al. (2014) GSM1350523 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/Readme.txt 56000 Julie Baker Enhancer chromatin signatures predict Smad2/3 binding in Xenopus In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic Julie Baker, Rakhi Gupta We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq 25205067 49423 SRP040298 WE - NF8 RNA-Seq NF8 embryo Gupta R et al. (2014) GSM1350522 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Ready ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56000/XENTR_10.0/RNA-Seq/Readme.txt 56169 Andrea Wills E2a is necessary for Smad2/3 dependent transcription and the direct repression of lefty We characterized the binding of Smad2/3 using ChIP-SEQ in both control gastrula-stage X. tropicalis embryos and embryos depleted of the transcription Andrea Wills, Andrea Wills, Julie Baker For ChIP-Seq, three biological replicates were performed for E2a-depleted X. tropicalis embryos, and two biological replicates were performed for control gastrula-stage embryos. For RNA-Seq, two biological replicates were performed for both E2a-depleted embryos and control embryos, and the mean expression levels were compared for each gene. 25669884 50519 SRP040548 WE - NF10.5 RNA-Seq NF10.5 embryo Wills AE et al. (2015) GSM1357039,GSM1357040 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/RNA-Seq/Readme.txt 56169 Andrea Wills E2a is necessary for Smad2/3 dependent transcription and the direct repression of lefty We characterized the binding of Smad2/3 using ChIP-SEQ in both control gastrula-stage X. tropicalis embryos and embryos depleted of the transcription Andrea Wills, Andrea Wills, Julie Baker For ChIP-Seq, three biological replicates were performed for E2a-depleted X. tropicalis embryos, and two biological replicates were performed for control gastrula-stage embryos. For RNA-Seq, two biological replicates were performed for both E2a-depleted embryos and control embryos, and the mean expression levels were compared for each gene. 25669884 50519 SRP040548 Smad2/3 WE - NF10.5 ChIP-Seq NF10.5 embryo Wills AE et al. (2015) GSM1357032,GSM1357033 ChIP-Seq/Transcription Factor/Smad2_3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq/Readme.txt 56169 Andrea Wills E2a is necessary for Smad2/3 dependent transcription and the direct repression of lefty We characterized the binding of Smad2/3 using ChIP-SEQ in both control gastrula-stage X. tropicalis embryos and embryos depleted of the transcription Andrea Wills, Andrea Wills, Julie Baker For ChIP-Seq, three biological replicates were performed for E2a-depleted X. tropicalis embryos, and two biological replicates were performed for control gastrula-stage embryos. For RNA-Seq, two biological replicates were performed for both E2a-depleted embryos and control embryos, and the mean expression levels were compared for each gene. 25669884 50519 SRP040548 input WE - NF10.5 ChIP-Seq NF10.5 embryo Wills AE et al. (2015) GSM1357037,GSM1357038 None tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq/Readme.txt 56169 Andrea Wills E2a is necessary for Smad2/3 dependent transcription and the direct repression of lefty We characterized the binding of Smad2/3 using ChIP-SEQ in both control gastrula-stage X. tropicalis embryos and embryos depleted of the transcription Andrea Wills, Andrea Wills, Julie Baker For ChIP-Seq, three biological replicates were performed for E2a-depleted X. tropicalis embryos, and two biological replicates were performed for control gastrula-stage embryos. For RNA-Seq, two biological replicates were performed for both E2a-depleted embryos and control embryos, and the mean expression levels were compared for each gene. 25669884 50519 SRP040548 Smad2/3 WE + tcf3 MO - NF10.5 ChIP-Seq NF10.5 embryo Wills AE et al. (2015) GSM1357034,GSM1357035,GSM1357036 ChIP-Seq/Transcription Factor/Smad2_3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq/Readme.txt 56169 Andrea Wills E2a is necessary for Smad2/3 dependent transcription and the direct repression of lefty We characterized the binding of Smad2/3 using ChIP-SEQ in both control gastrula-stage X. tropicalis embryos and embryos depleted of the transcription Andrea Wills, Andrea Wills, Julie Baker For ChIP-Seq, three biological replicates were performed for E2a-depleted X. tropicalis embryos, and two biological replicates were performed for control gastrula-stage embryos. For RNA-Seq, two biological replicates were performed for both E2a-depleted embryos and control embryos, and the mean expression levels were compared for each gene. 25669884 50519 SRP040548 Smad2/3 WE + tcf3 MO - NF10.5 ChIP-Seq NF10.5 embryo Wills AE et al. (2015) GSM1357034,GSM1357035,GSM1357036 Manipulations/Morpholino tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq/Readme.txt 56169 Andrea Wills E2a is necessary for Smad2/3 dependent transcription and the direct repression of lefty We characterized the binding of Smad2/3 using ChIP-SEQ in both control gastrula-stage X. tropicalis embryos and embryos depleted of the transcription Andrea Wills, Andrea Wills, Julie Baker For ChIP-Seq, three biological replicates were performed for E2a-depleted X. tropicalis embryos, and two biological replicates were performed for control gastrula-stage embryos. For RNA-Seq, two biological replicates were performed for both E2a-depleted embryos and control embryos, and the mean expression levels were compared for each gene. 25669884 50519 SRP040548 WE + tcf3 MO - NF10.5 RNA-Seq NF10.5 embryo Wills AE et al. (2015) GSM1357041,GSM1357042 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/RNA-Seq/Readme.txt 56169 Andrea Wills E2a is necessary for Smad2/3 dependent transcription and the direct repression of lefty We characterized the binding of Smad2/3 using ChIP-SEQ in both control gastrula-stage X. tropicalis embryos and embryos depleted of the transcription Andrea Wills, Andrea Wills, Julie Baker For ChIP-Seq, three biological replicates were performed for E2a-depleted X. tropicalis embryos, and two biological replicates were performed for control gastrula-stage embryos. For RNA-Seq, two biological replicates were performed for both E2a-depleted embryos and control embryos, and the mean expression levels were compared for each gene. 25669884 50519 SRP040548 WE + tcf3 MO - NF10.5 RNA-Seq NF10.5 embryo Wills AE et al. (2015) GSM1357041,GSM1357042 Manipulations/Morpholino tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56169/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF5 (2.5hpf) - Series3 RNA-Seq NF5 embryo Collart C et al. (2014) GSM1357570 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF9 (7.0hpf) - Series3 rd RNA-Seq NF9 embryo Collart C et al. (2014) GSM1357591 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF9 (8.0hpf) - Series3 RNA-Seq NF9 embryo Collart C et al. (2014) GSM1357581 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF1 (0.0hpf) - Series3 rd RNA-Seq NF1 zygote Collart C et al. (2014) GSM1357584 RNA-Seq/Embryonic Tissues/fertilized egg tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF1 (0.0hpf) - Series1 RNA-Seq NF1 zygote Collart C et al. (2014) GSM1357541 RNA-Seq/Embryonic Tissues/fertilized egg tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF4 (2.0hpf) - Series3 rd RNA-Seq NF4 embryo Collart C et al. (2014) GSM1357586 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF2 (1.0hpf) - Series3 rd RNA-Seq NF2 embryo Collart C et al. (2014) GSM1357585 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF10 (9.0hpf) - Series3 RNA-Seq NF10 embryo Collart C et al. (2014) GSM1357583 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF11.5 (9.5hpf) - Series2 RNA-Seq NF11.5 embryo Collart C et al. (2014) GSM1357562 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF7 (3.0hpf) - Series1 RNA-Seq NF7 embryo Collart C et al. (2014) GSM1357547 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF8 (6.5hpf) - Series3 RNA-Seq NF8 embryo Collart C et al. (2014) GSM1357578 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF11 (9.0hpf) - Series2 RNA-Seq NF11 embryo Collart C et al. (2014) GSM1357561 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF2 (1.0hpf) - Series3 RNA-Seq NF2 embryo Collart C et al. (2014) GSM1357567 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF2 (1.5hpf) - Series3 RNA-Seq NF2 embryo Collart C et al. (2014) GSM1357568 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF3 (1.5hpf) - Series1 RNA-Seq NF3 embryo Collart C et al. (2014) GSM1357544 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF4 (2.0hpf) - Series3 RNA-Seq NF4 embryo Collart C et al. (2014) GSM1357569 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF5 (2.0hpf) - Series1 RNA-Seq NF5 embryo Collart C et al. (2014) GSM1357545 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF6 (3.0hpf) - Series3 rd RNA-Seq NF6 embryo Collart C et al. (2014) GSM1357587 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF6 (2.5hpf) - Series1 RNA-Seq NF6 embryo Collart C et al. (2014) GSM1357546 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF6 (3.0hpf) - Series3 RNA-Seq NF6 embryo Collart C et al. (2014) GSM1357571 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF6 (3.5hpf) - Series3 RNA-Seq NF6 embryo Collart C et al. (2014) GSM1357572 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF7 (4.0hpf) - Series3 rd RNA-Seq NF7 embryo Collart C et al. (2014) GSM1357588 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF7 (3.0hpf) - Series2 RNA-Seq NF7 embryo Collart C et al. (2014) GSM1357549 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF6 (2.5hpf) - Series2 RNA-Seq NF6 embryo Collart C et al. (2014) GSM1357548 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF7 (4.0hpf) - Series3 RNA-Seq NF7 embryo Collart C et al. (2014) GSM1357573 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF7 (4.5hpf) - Series3 RNA-Seq NF7 embryo Collart C et al. (2014) GSM1357574 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF8 (4.0hpf) - Series2 RNA-Seq NF8 embryo Collart C et al. (2014) GSM1357551 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF8 (4.5hpf) - Series2 RNA-Seq NF8 embryo Collart C et al. (2014) GSM1357552,GSM1357563 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF8 (5.0hpf) - Series2 RNA-Seq NF8 embryo Collart C et al. (2014) GSM1357553 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF8 (5.0hpf) - Series3 RNA-Seq NF8 embryo Collart C et al. (2014) GSM1357575 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF8 (5.5hpf) - Series3 RNA-Seq NF8 embryo Collart C et al. (2014) GSM1357576 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF8 (6.0hpf) - Series3 RNA-Seq NF8 embryo Collart C et al. (2014) GSM1357577 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF9 (8.0hpf) - Series3 rd RNA-Seq NF9 embryo Collart C et al. (2014) GSM1357592 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF9 (6.0hpf) - Series2 RNA-Seq NF9 embryo Collart C et al. (2014) GSM1357555 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF9 (6.5hpf) - Series2 RNA-Seq NF9 embryo Collart C et al. (2014) GSM1357556,GSM1357564 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF7 (3.5hpf) - Series2 RNA-Seq NF7 embryo Collart C et al. (2014) GSM1357550 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF9 (7.0hpf) - Series3 RNA-Seq NF9 embryo Collart C et al. (2014) GSM1357579 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF9 (7.5hpf) - Series3 RNA-Seq NF9 embryo Collart C et al. (2014) GSM1357580 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF9 (8.5hpf) - Series3 RNA-Seq NF9 embryo Collart C et al. (2014) GSM1357582 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF1 (0.0hpf) - Series3 RNA-Seq NF1 zygote Collart C et al. (2014) GSM1357565 RNA-Seq/Embryonic Tissues/fertilized egg tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF9 (5.5hpf) - Series2 RNA-Seq NF9 embryo Collart C et al. (2014) GSM1357554 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF8 (6.0hpf) - Series3 rd RNA-Seq NF8 embryo Collart C et al. (2014) GSM1357590 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF2 (1.0hpf) - Series1 RNA-Seq NF2 embryo Collart C et al. (2014) GSM1357543 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF1 (0.5hpf) - Series1 RNA-Seq NF1 embryo Collart C et al. (2014) GSM1357542 RNA-Seq/Whole Embryo/fertilized egg tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF8 (5.0hpf) - Series3 rd RNA-Seq NF8 embryo Collart C et al. (2014) GSM1357589 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF10.25 (7.5hpf) - Series2 RNA-Seq NF10.25 embryo Collart C et al. (2014) GSM1357558 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF10 (7.0hpf) - Series2 RNA-Seq NF10 embryo Collart C et al. (2014) GSM1357557 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF1 (0.5hpf) - Series3 RNA-Seq NF1 embryo Collart C et al. (2014) GSM1357566 RNA-Seq/Whole Embryo/fertilized egg tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF10.5 (8.0hpf) - Series2 RNA-Seq NF10.5 embryo Collart C et al. (2014) GSM1357559 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56242 Mike Gilchrist High-resolution analysis of gene activity during the Xenopus mid-blastula transition The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization 24757007 48872 SRP040589 WE - NF10.5 (8.5hpf) - Series2 RNA-Seq NF10.5 embryo Collart C et al. (2014) GSM1357560 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56242/XENTR_10.0/RNA-Seq/Readme.txt 56586 Gert Jan Veenstra Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs Recent developments in genomic sequencing technology have enabled comprehensive transcriptome analyses of single cells. In contrast, single cell prote Gert Jan Veenstra, Arne Smits, Rik Lindeboom, Matteo Perino, Simon van Heeringen, GertJan Veenstra, Michiel Vermeulen RNA-seq in Xenopus laevis of 5 replicates of both single eggs and single embryos. 25056316 49279 SRP041021 WE - NF1 rd RNA-Seq NF1 zygote Smits AH et al. (2014) GSM1364749,GSM1364750,GSM1364751,GSM1364752,GSM1364753 RNA-Seq/Embryonic Tissues/fertilized egg laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56586 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56586/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56586/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56586/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56586/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56586/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56586/XENLA_10.1/RNA-Seq/Readme.txt 56586 Gert Jan Veenstra Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs Recent developments in genomic sequencing technology have enabled comprehensive transcriptome analyses of single cells. In contrast, single cell prote Gert Jan Veenstra, Arne Smits, Rik Lindeboom, Matteo Perino, Simon van Heeringen, GertJan Veenstra, Michiel Vermeulen RNA-seq in Xenopus laevis of 5 replicates of both single eggs and single embryos. 25056316 49279 SRP041021 WE - NF10.5 rd RNA-Seq NF10.5 embryo Smits AH et al. (2014) GSM1430926,GSM1430927,GSM1430928,GSM1430929,GSM1430930 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56586 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56586/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56586/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56586/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56586/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56586/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56586/XENLA_10.1/RNA-Seq/Readme.txt 56586 Gert Jan Veenstra Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs Recent developments in genomic sequencing technology have enabled comprehensive transcriptome analyses of single cells. In contrast, single cell prote Gert Jan Veenstra, Arne Smits, Rik Lindeboom, Matteo Perino, Simon van Heeringen, GertJan Veenstra, Michiel Vermeulen RNA-seq in Xenopus laevis of 5 replicates of both single eggs and single embryos. 25056316 49279 SRP041021 WE - NF10.5 rd technical rep RNA-Seq NF10.5 embryo Smits AH et al. (2014) GSM1430931,GSM1430932,GSM1430933 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56586 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56586/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56586/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56586/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56586/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56586/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56586/XENLA_10.1/RNA-Seq/Readme.txt 56680 Maria Warnefors MicroRNA editing in Xenopus tropicalis We collected small RNA sequencing data from brain and heart of an adult Xenopus tropicalis individual to investigate the conservation of site-specific Maria Warnefors, Angélica Liechti, Jean Halbert, Delphine Valloton, Henrik Kaessmann Sequencing of 2 small RNA sequencing libraries 24964909 50469 SRP041076 brain - adult miRNA-Seq adult brain Warnefors M et al. (2014) GSM1366781 miRNA-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56680 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56680/XENTR_10.0/miRNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56680/XENTR_10.0/miRNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56680/XENTR_10.0/miRNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56680/XENTR_10.0/miRNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56680/XENTR_10.0/miRNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56680/XENTR_10.0/miRNA-Seq/Readme.txt 56680 Maria Warnefors MicroRNA editing in Xenopus tropicalis We collected small RNA sequencing data from brain and heart of an adult Xenopus tropicalis individual to investigate the conservation of site-specific Maria Warnefors, Angélica Liechti, Jean Halbert, Delphine Valloton, Henrik Kaessmann Sequencing of 2 small RNA sequencing libraries 24964909 50469 SRP041076 heart - adult miRNA-Seq adult heart Warnefors M et al. (2014) GSM1366782 miRNA-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56680 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56680/XENTR_10.0/miRNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56680/XENTR_10.0/miRNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56680/XENTR_10.0/miRNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56680/XENTR_10.0/miRNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56680/XENTR_10.0/miRNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE56680/XENTR_10.0/miRNA-Seq/Readme.txt 58420 Gabriela Salinas-Riester Next generation sequencing identifies differentially localized transcripts in Xenopus laevis and Xenopus tropicalis oocytes RNA-seq technology was used to identify differentially localized transcripts from Xenopus laevis and Xenopus tropicalis stage VI oocytes. Besides the Gabriela Salinas-Riester, Maike Claußen, Tomas Pieler mRNA profiles of Xenopus laevis and Xenopus tropicalis animal and vegetal oocyte halves were generated by RNA-seq technology. For Xenopus laevis, animal and vegetal oocyte RNA preparations from two different females were generated in duplicates. For Xenopus tropicalis, animal and vegetal oocyte RNA preparations from two different females were analyzed. 26337391 51224 SRP043147 animal oocyte - oocyte VI RNA-Seq oocyte VI animal Claußen M et al. (2015) GSM1410597,GSM1410598,GSM1410599,GSM1410600 RNA-Seq/Embryonic Tissues/unfertilized egg laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420/XENLA_10.1/RNA-Seq/Readme.txt 58420 Gabriela Salinas-Riester Next generation sequencing identifies differentially localized transcripts in Xenopus laevis and Xenopus tropicalis oocytes RNA-seq technology was used to identify differentially localized transcripts from Xenopus laevis and Xenopus tropicalis stage VI oocytes. Besides the Gabriela Salinas-Riester, Maike Claußen, Tomas Pieler mRNA profiles of Xenopus laevis and Xenopus tropicalis animal and vegetal oocyte halves were generated by RNA-seq technology. For Xenopus laevis, animal and vegetal oocyte RNA preparations from two different females were generated in duplicates. For Xenopus tropicalis, animal and vegetal oocyte RNA preparations from two different females were analyzed. 26337391 51224 SRP043147 vegetal oocyte - oocyte VI RNA-Seq oocyte VI oocyte Claußen M et al. (2015) GSM1410601,GSM1410602,GSM1410603,GSM1410604 RNA-Seq/Embryonic Tissues/unfertilized egg laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420/XENLA_10.1/RNA-Seq/Readme.txt 58420 Gabriela Salinas-Riester Next generation sequencing identifies differentially localized transcripts in Xenopus laevis and Xenopus tropicalis oocytes RNA-seq technology was used to identify differentially localized transcripts from Xenopus laevis and Xenopus tropicalis stage VI oocytes. Besides the Gabriela Salinas-Riester, Maike Claußen, Tomas Pieler mRNA profiles of Xenopus laevis and Xenopus tropicalis animal and vegetal oocyte halves were generated by RNA-seq technology. For Xenopus laevis, animal and vegetal oocyte RNA preparations from two different females were generated in duplicates. For Xenopus tropicalis, animal and vegetal oocyte RNA preparations from two different females were analyzed. 26337391 51224 SRP043147 vegetal oocyte - oocyte VI RNA-Seq oocyte VI oocyte Claußen M et al. (2015) GSM1410607,GSM1410608 RNA-Seq/Embryonic Tissues/unfertilized egg tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420/XENTR_10.0/RNA-Seq/Readme.txt 58420 Gabriela Salinas-Riester Next generation sequencing identifies differentially localized transcripts in Xenopus laevis and Xenopus tropicalis oocytes RNA-seq technology was used to identify differentially localized transcripts from Xenopus laevis and Xenopus tropicalis stage VI oocytes. Besides the Gabriela Salinas-Riester, Maike Claußen, Tomas Pieler mRNA profiles of Xenopus laevis and Xenopus tropicalis animal and vegetal oocyte halves were generated by RNA-seq technology. For Xenopus laevis, animal and vegetal oocyte RNA preparations from two different females were generated in duplicates. For Xenopus tropicalis, animal and vegetal oocyte RNA preparations from two different females were analyzed. 26337391 51224 SRP043147 animal oocyte - oocyte VI RNA-Seq oocyte VI animal Claußen M et al. (2015) GSM1410605,GSM1410606 RNA-Seq/Embryonic Tissues/unfertilized egg tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE58420/XENTR_10.0/RNA-Seq/Readme.txt 59309 Ian Quigley Multicilin drives centriole biogenesis via E2f proteins Biochemistry suggests e2f4 forms a complex with the coiled-coiled protein multicilin (MCIDAS), a protein that is necessary and sufficient to specify m Ian Quigley, Lina Ma, Chris Kintner RNAseq: misexpression of multicilin-HGR +/- dominant-negative e2f4 messenger RNAs in X. laevis animal caps, multicilin induced with dexamethasone at mid-stage 11 and harvested at 3 timepoints (3, 6, and 9 hours after induction, roughly corresponding to stages 13, 16, and 18) with 3 biological replicates. ChIPseq: misexpression of e2f4-GFP +/- multicilin-HGR messenger RNAs in X. laevis animal caps, multicilin induced at mid-stage 11 and harvested at one timepoint (6 hours after induction, roughly corresponding to stage 16), immunoprecipitated with anti-GFP and sequenced; 2 biological replicates. Background was input prior to IP. 24934224 49750 SRP044238 e2f4 animal cap - NF16 ChIP-Seq NF16 animal cap Ma L et al. (2014) GSM1434789 ChIP-Seq/Transcription Factor/E2F4 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/Readme.txt 59309 Ian Quigley Multicilin drives centriole biogenesis via E2f proteins Biochemistry suggests e2f4 forms a complex with the coiled-coiled protein multicilin (MCIDAS), a protein that is necessary and sufficient to specify m Ian Quigley, Lina Ma, Chris Kintner RNAseq: misexpression of multicilin-HGR +/- dominant-negative e2f4 messenger RNAs in X. laevis animal caps, multicilin induced with dexamethasone at mid-stage 11 and harvested at 3 timepoints (3, 6, and 9 hours after induction, roughly corresponding to stages 13, 16, and 18) with 3 biological replicates. ChIPseq: misexpression of e2f4-GFP +/- multicilin-HGR messenger RNAs in X. laevis animal caps, multicilin induced at mid-stage 11 and harvested at one timepoint (6 hours after induction, roughly corresponding to stage 16), immunoprecipitated with anti-GFP and sequenced; 2 biological replicates. Background was input prior to IP. 24934224 49750 SRP044238 e2f4 animal cap - NF16 ChIP-Seq NF16 animal cap Ma L et al. (2014) GSM1434789 Manipulations/mRNA Injection laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/Readme.txt 59309 Ian Quigley Multicilin drives centriole biogenesis via E2f proteins Biochemistry suggests e2f4 forms a complex with the coiled-coiled protein multicilin (MCIDAS), a protein that is necessary and sufficient to specify m Ian Quigley, Lina Ma, Chris Kintner RNAseq: misexpression of multicilin-HGR +/- dominant-negative e2f4 messenger RNAs in X. laevis animal caps, multicilin induced with dexamethasone at mid-stage 11 and harvested at 3 timepoints (3, 6, and 9 hours after induction, roughly corresponding to stages 13, 16, and 18) with 3 biological replicates. ChIPseq: misexpression of e2f4-GFP +/- multicilin-HGR messenger RNAs in X. laevis animal caps, multicilin induced at mid-stage 11 and harvested at one timepoint (6 hours after induction, roughly corresponding to stage 16), immunoprecipitated with anti-GFP and sequenced; 2 biological replicates. Background was input prior to IP. 24934224 49750 SRP044238 animal cap + mcidas - NF13 RNA-Seq NF13 animal cap Ma L et al. (2014) GSM1434771,GSM1434772,GSM1434773 Manipulations/mRNA Injection laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/Readme.txt 59309 Ian Quigley Multicilin drives centriole biogenesis via E2f proteins Biochemistry suggests e2f4 forms a complex with the coiled-coiled protein multicilin (MCIDAS), a protein that is necessary and sufficient to specify m Ian Quigley, Lina Ma, Chris Kintner RNAseq: misexpression of multicilin-HGR +/- dominant-negative e2f4 messenger RNAs in X. laevis animal caps, multicilin induced with dexamethasone at mid-stage 11 and harvested at 3 timepoints (3, 6, and 9 hours after induction, roughly corresponding to stages 13, 16, and 18) with 3 biological replicates. ChIPseq: misexpression of e2f4-GFP +/- multicilin-HGR messenger RNAs in X. laevis animal caps, multicilin induced at mid-stage 11 and harvested at one timepoint (6 hours after induction, roughly corresponding to stage 16), immunoprecipitated with anti-GFP and sequenced; 2 biological replicates. Background was input prior to IP. 24934224 49750 SRP044238 animal cap + mcidas - NF13 RNA-Seq NF13 animal cap Ma L et al. (2014) GSM1434771,GSM1434772,GSM1434773 RNA-Seq/Embryonic Tissues/Neurula NF13 to NF21/animal cap laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/Readme.txt 59309 Ian Quigley Multicilin drives centriole biogenesis via E2f proteins Biochemistry suggests e2f4 forms a complex with the coiled-coiled protein multicilin (MCIDAS), a protein that is necessary and sufficient to specify m Ian Quigley, Lina Ma, Chris Kintner RNAseq: misexpression of multicilin-HGR +/- dominant-negative e2f4 messenger RNAs in X. laevis animal caps, multicilin induced with dexamethasone at mid-stage 11 and harvested at 3 timepoints (3, 6, and 9 hours after induction, roughly corresponding to stages 13, 16, and 18) with 3 biological replicates. ChIPseq: misexpression of e2f4-GFP +/- multicilin-HGR messenger RNAs in X. laevis animal caps, multicilin induced at mid-stage 11 and harvested at one timepoint (6 hours after induction, roughly corresponding to stage 16), immunoprecipitated with anti-GFP and sequenced; 2 biological replicates. Background was input prior to IP. 24934224 49750 SRP044238 e2f4 animal cap + mcidas - NF16 ChIP-Seq NF16 animal cap Ma L et al. (2014) GSM1434790 ChIP-Seq/Transcription Factor/E2F4 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/Readme.txt 59309 Ian Quigley Multicilin drives centriole biogenesis via E2f proteins Biochemistry suggests e2f4 forms a complex with the coiled-coiled protein multicilin (MCIDAS), a protein that is necessary and sufficient to specify m Ian Quigley, Lina Ma, Chris Kintner RNAseq: misexpression of multicilin-HGR +/- dominant-negative e2f4 messenger RNAs in X. laevis animal caps, multicilin induced with dexamethasone at mid-stage 11 and harvested at 3 timepoints (3, 6, and 9 hours after induction, roughly corresponding to stages 13, 16, and 18) with 3 biological replicates. ChIPseq: misexpression of e2f4-GFP +/- multicilin-HGR messenger RNAs in X. laevis animal caps, multicilin induced at mid-stage 11 and harvested at one timepoint (6 hours after induction, roughly corresponding to stage 16), immunoprecipitated with anti-GFP and sequenced; 2 biological replicates. Background was input prior to IP. 24934224 49750 SRP044238 e2f4 animal cap + mcidas - NF16 ChIP-Seq NF16 animal cap Ma L et al. (2014) GSM1434790 Manipulations/mRNA Injection laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/Readme.txt 59309 Ian Quigley Multicilin drives centriole biogenesis via E2f proteins Biochemistry suggests e2f4 forms a complex with the coiled-coiled protein multicilin (MCIDAS), a protein that is necessary and sufficient to specify m Ian Quigley, Lina Ma, Chris Kintner RNAseq: misexpression of multicilin-HGR +/- dominant-negative e2f4 messenger RNAs in X. laevis animal caps, multicilin induced with dexamethasone at mid-stage 11 and harvested at 3 timepoints (3, 6, and 9 hours after induction, roughly corresponding to stages 13, 16, and 18) with 3 biological replicates. ChIPseq: misexpression of e2f4-GFP +/- multicilin-HGR messenger RNAs in X. laevis animal caps, multicilin induced at mid-stage 11 and harvested at one timepoint (6 hours after induction, roughly corresponding to stage 16), immunoprecipitated with anti-GFP and sequenced; 2 biological replicates. Background was input prior to IP. 24934224 49750 SRP044238 input animal cap - NF16 ChIP-Seq NF16 animal cap Ma L et al. (2014) GSM1434791 None laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/Readme.txt 59309 Ian Quigley Multicilin drives centriole biogenesis via E2f proteins Biochemistry suggests e2f4 forms a complex with the coiled-coiled protein multicilin (MCIDAS), a protein that is necessary and sufficient to specify m Ian Quigley, Lina Ma, Chris Kintner RNAseq: misexpression of multicilin-HGR +/- dominant-negative e2f4 messenger RNAs in X. laevis animal caps, multicilin induced with dexamethasone at mid-stage 11 and harvested at 3 timepoints (3, 6, and 9 hours after induction, roughly corresponding to stages 13, 16, and 18) with 3 biological replicates. ChIPseq: misexpression of e2f4-GFP +/- multicilin-HGR messenger RNAs in X. laevis animal caps, multicilin induced at mid-stage 11 and harvested at one timepoint (6 hours after induction, roughly corresponding to stage 16), immunoprecipitated with anti-GFP and sequenced; 2 biological replicates. Background was input prior to IP. 24934224 49750 SRP044238 animal cap + mcidas - NF18 RNA-Seq NF18 animal cap Ma L et al. (2014) GSM1434783,GSM1434784,GSM1434785 Manipulations/mRNA Injection laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/Readme.txt 59309 Ian Quigley Multicilin drives centriole biogenesis via E2f proteins Biochemistry suggests e2f4 forms a complex with the coiled-coiled protein multicilin (MCIDAS), a protein that is necessary and sufficient to specify m Ian Quigley, Lina Ma, Chris Kintner RNAseq: misexpression of multicilin-HGR +/- dominant-negative e2f4 messenger RNAs in X. laevis animal caps, multicilin induced with dexamethasone at mid-stage 11 and harvested at 3 timepoints (3, 6, and 9 hours after induction, roughly corresponding to stages 13, 16, and 18) with 3 biological replicates. ChIPseq: misexpression of e2f4-GFP +/- multicilin-HGR messenger RNAs in X. laevis animal caps, multicilin induced at mid-stage 11 and harvested at one timepoint (6 hours after induction, roughly corresponding to stage 16), immunoprecipitated with anti-GFP and sequenced; 2 biological replicates. Background was input prior to IP. 24934224 49750 SRP044238 animal cap + mcidas - NF18 RNA-Seq NF18 animal cap Ma L et al. (2014) GSM1434783,GSM1434784,GSM1434785 RNA-Seq/Embryonic Tissues/Neurula NF13 to NF21/animal cap laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/Readme.txt 59309 Ian Quigley Multicilin drives centriole biogenesis via E2f proteins Biochemistry suggests e2f4 forms a complex with the coiled-coiled protein multicilin (MCIDAS), a protein that is necessary and sufficient to specify m Ian Quigley, Lina Ma, Chris Kintner RNAseq: misexpression of multicilin-HGR +/- dominant-negative e2f4 messenger RNAs in X. laevis animal caps, multicilin induced with dexamethasone at mid-stage 11 and harvested at 3 timepoints (3, 6, and 9 hours after induction, roughly corresponding to stages 13, 16, and 18) with 3 biological replicates. ChIPseq: misexpression of e2f4-GFP +/- multicilin-HGR messenger RNAs in X. laevis animal caps, multicilin induced at mid-stage 11 and harvested at one timepoint (6 hours after induction, roughly corresponding to stage 16), immunoprecipitated with anti-GFP and sequenced; 2 biological replicates. Background was input prior to IP. 24934224 49750 SRP044238 animal cap + mcidas + DNe2f4 - NF13 RNA-Seq NF13 animal cap Ma L et al. (2014) GSM1434774,GSM1434775,GSM1434776 Manipulations/mRNA Injection laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/Readme.txt 59309 Ian Quigley Multicilin drives centriole biogenesis via E2f proteins Biochemistry suggests e2f4 forms a complex with the coiled-coiled protein multicilin (MCIDAS), a protein that is necessary and sufficient to specify m Ian Quigley, Lina Ma, Chris Kintner RNAseq: misexpression of multicilin-HGR +/- dominant-negative e2f4 messenger RNAs in X. laevis animal caps, multicilin induced with dexamethasone at mid-stage 11 and harvested at 3 timepoints (3, 6, and 9 hours after induction, roughly corresponding to stages 13, 16, and 18) with 3 biological replicates. ChIPseq: misexpression of e2f4-GFP +/- multicilin-HGR messenger RNAs in X. laevis animal caps, multicilin induced at mid-stage 11 and harvested at one timepoint (6 hours after induction, roughly corresponding to stage 16), immunoprecipitated with anti-GFP and sequenced; 2 biological replicates. Background was input prior to IP. 24934224 49750 SRP044238 animal cap + mcidas + DNe2f4 - NF13 RNA-Seq NF13 animal cap Ma L et al. (2014) GSM1434774,GSM1434775,GSM1434776 RNA-Seq/Embryonic Tissues/Neurula NF13 to NF21/animal cap laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/Readme.txt 59309 Ian Quigley Multicilin drives centriole biogenesis via E2f proteins Biochemistry suggests e2f4 forms a complex with the coiled-coiled protein multicilin (MCIDAS), a protein that is necessary and sufficient to specify m Ian Quigley, Lina Ma, Chris Kintner RNAseq: misexpression of multicilin-HGR +/- dominant-negative e2f4 messenger RNAs in X. laevis animal caps, multicilin induced with dexamethasone at mid-stage 11 and harvested at 3 timepoints (3, 6, and 9 hours after induction, roughly corresponding to stages 13, 16, and 18) with 3 biological replicates. ChIPseq: misexpression of e2f4-GFP +/- multicilin-HGR messenger RNAs in X. laevis animal caps, multicilin induced at mid-stage 11 and harvested at one timepoint (6 hours after induction, roughly corresponding to stage 16), immunoprecipitated with anti-GFP and sequenced; 2 biological replicates. Background was input prior to IP. 24934224 49750 SRP044238 input animal cap + mcidas - NF16 ChIP-Seq NF16 animal cap Ma L et al. (2014) GSM1434792 None laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/ChIP-Seq/Readme.txt 59309 Ian Quigley Multicilin drives centriole biogenesis via E2f proteins Biochemistry suggests e2f4 forms a complex with the coiled-coiled protein multicilin (MCIDAS), a protein that is necessary and sufficient to specify m Ian Quigley, Lina Ma, Chris Kintner RNAseq: misexpression of multicilin-HGR +/- dominant-negative e2f4 messenger RNAs in X. laevis animal caps, multicilin induced with dexamethasone at mid-stage 11 and harvested at 3 timepoints (3, 6, and 9 hours after induction, roughly corresponding to stages 13, 16, and 18) with 3 biological replicates. ChIPseq: misexpression of e2f4-GFP +/- multicilin-HGR messenger RNAs in X. laevis animal caps, multicilin induced at mid-stage 11 and harvested at one timepoint (6 hours after induction, roughly corresponding to stage 16), immunoprecipitated with anti-GFP and sequenced; 2 biological replicates. Background was input prior to IP. 24934224 49750 SRP044238 animal cap + mcidas - NF16 RNA-Seq NF16 animal cap Ma L et al. (2014) GSM1434777,GSM1434778,GSM1434779 Manipulations/mRNA Injection laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/Readme.txt 59309 Ian Quigley Multicilin drives centriole biogenesis via E2f proteins Biochemistry suggests e2f4 forms a complex with the coiled-coiled protein multicilin (MCIDAS), a protein that is necessary and sufficient to specify m Ian Quigley, Lina Ma, Chris Kintner RNAseq: misexpression of multicilin-HGR +/- dominant-negative e2f4 messenger RNAs in X. laevis animal caps, multicilin induced with dexamethasone at mid-stage 11 and harvested at 3 timepoints (3, 6, and 9 hours after induction, roughly corresponding to stages 13, 16, and 18) with 3 biological replicates. ChIPseq: misexpression of e2f4-GFP +/- multicilin-HGR messenger RNAs in X. laevis animal caps, multicilin induced at mid-stage 11 and harvested at one timepoint (6 hours after induction, roughly corresponding to stage 16), immunoprecipitated with anti-GFP and sequenced; 2 biological replicates. Background was input prior to IP. 24934224 49750 SRP044238 animal cap + mcidas - NF16 RNA-Seq NF16 animal cap Ma L et al. (2014) GSM1434777,GSM1434778,GSM1434779 RNA-Seq/Embryonic Tissues/Neurula NF13 to NF21/animal cap laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/Readme.txt 59309 Ian Quigley Multicilin drives centriole biogenesis via E2f proteins Biochemistry suggests e2f4 forms a complex with the coiled-coiled protein multicilin (MCIDAS), a protein that is necessary and sufficient to specify m Ian Quigley, Lina Ma, Chris Kintner RNAseq: misexpression of multicilin-HGR +/- dominant-negative e2f4 messenger RNAs in X. laevis animal caps, multicilin induced with dexamethasone at mid-stage 11 and harvested at 3 timepoints (3, 6, and 9 hours after induction, roughly corresponding to stages 13, 16, and 18) with 3 biological replicates. ChIPseq: misexpression of e2f4-GFP +/- multicilin-HGR messenger RNAs in X. laevis animal caps, multicilin induced at mid-stage 11 and harvested at one timepoint (6 hours after induction, roughly corresponding to stage 16), immunoprecipitated with anti-GFP and sequenced; 2 biological replicates. Background was input prior to IP. 24934224 49750 SRP044238 animal cap + mcidas + DNe2f4 - NF16 RNA-Seq NF16 animal cap Ma L et al. (2014) GSM1434780,GSM1434781,GSM1434782 Manipulations/mRNA Injection laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/Readme.txt 59309 Ian Quigley Multicilin drives centriole biogenesis via E2f proteins Biochemistry suggests e2f4 forms a complex with the coiled-coiled protein multicilin (MCIDAS), a protein that is necessary and sufficient to specify m Ian Quigley, Lina Ma, Chris Kintner RNAseq: misexpression of multicilin-HGR +/- dominant-negative e2f4 messenger RNAs in X. laevis animal caps, multicilin induced with dexamethasone at mid-stage 11 and harvested at 3 timepoints (3, 6, and 9 hours after induction, roughly corresponding to stages 13, 16, and 18) with 3 biological replicates. ChIPseq: misexpression of e2f4-GFP +/- multicilin-HGR messenger RNAs in X. laevis animal caps, multicilin induced at mid-stage 11 and harvested at one timepoint (6 hours after induction, roughly corresponding to stage 16), immunoprecipitated with anti-GFP and sequenced; 2 biological replicates. Background was input prior to IP. 24934224 49750 SRP044238 animal cap + mcidas + DNe2f4 - NF16 RNA-Seq NF16 animal cap Ma L et al. (2014) GSM1434780,GSM1434781,GSM1434782 RNA-Seq/Embryonic Tissues/Neurula NF13 to NF21/animal cap laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/Readme.txt 59309 Ian Quigley Multicilin drives centriole biogenesis via E2f proteins Biochemistry suggests e2f4 forms a complex with the coiled-coiled protein multicilin (MCIDAS), a protein that is necessary and sufficient to specify m Ian Quigley, Lina Ma, Chris Kintner RNAseq: misexpression of multicilin-HGR +/- dominant-negative e2f4 messenger RNAs in X. laevis animal caps, multicilin induced with dexamethasone at mid-stage 11 and harvested at 3 timepoints (3, 6, and 9 hours after induction, roughly corresponding to stages 13, 16, and 18) with 3 biological replicates. ChIPseq: misexpression of e2f4-GFP +/- multicilin-HGR messenger RNAs in X. laevis animal caps, multicilin induced at mid-stage 11 and harvested at one timepoint (6 hours after induction, roughly corresponding to stage 16), immunoprecipitated with anti-GFP and sequenced; 2 biological replicates. Background was input prior to IP. 24934224 49750 SRP044238 animal cap + mcidas + DNe2f4 - NF18 RNA-Seq NF18 animal cap Ma L et al. (2014) GSM1434786,GSM1434787,GSM1434788 Manipulations/mRNA Injection laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/Readme.txt 59309 Ian Quigley Multicilin drives centriole biogenesis via E2f proteins Biochemistry suggests e2f4 forms a complex with the coiled-coiled protein multicilin (MCIDAS), a protein that is necessary and sufficient to specify m Ian Quigley, Lina Ma, Chris Kintner RNAseq: misexpression of multicilin-HGR +/- dominant-negative e2f4 messenger RNAs in X. laevis animal caps, multicilin induced with dexamethasone at mid-stage 11 and harvested at 3 timepoints (3, 6, and 9 hours after induction, roughly corresponding to stages 13, 16, and 18) with 3 biological replicates. ChIPseq: misexpression of e2f4-GFP +/- multicilin-HGR messenger RNAs in X. laevis animal caps, multicilin induced at mid-stage 11 and harvested at one timepoint (6 hours after induction, roughly corresponding to stage 16), immunoprecipitated with anti-GFP and sequenced; 2 biological replicates. Background was input prior to IP. 24934224 49750 SRP044238 animal cap + mcidas + DNe2f4 - NF18 RNA-Seq NF18 animal cap Ma L et al. (2014) GSM1434786,GSM1434787,GSM1434788 RNA-Seq/Embryonic Tissues/Neurula NF13 to NF21/animal cap laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE59309/XENLA_10.1/RNA-Seq/Readme.txt 63228 Nelson Lau Xenopus Piwi protein associated transcripts indicate regulation beyond transposons This study examines the population of transcripts associated with the Xenopus Piwi proteins, Xiwi and Xili, from X.laevis and X.tropicalis. RIP-seq, C Nelson Lau, Trey Toombs, Yuliya Sytnkova, Gungwei Chirn, Michael Blower We performed several replicates of a Piw CLIP-Seq experiment to isolate RNA fragments as CLIP-tags to discover which transcripts are preferentially bound by the Piwi protein. Then we performed several types of mRNA expression profiling experiments using several forms of mRNA-Seq library construction formats. Finally, we sequenced the piRNAs from the OSS cells 28031481 52877 SRP049739 piwil1 oocyte - adult RIP-Seq adult oocyte Toombs JA et al. (2017) GSM1544078 RIP-Seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/RIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/RIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/RIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/RIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/RIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/RIP-Seq/Readme.txt 63228 Nelson Lau Xenopus Piwi protein associated transcripts indicate regulation beyond transposons This study examines the population of transcripts associated with the Xenopus Piwi proteins, Xiwi and Xili, from X.laevis and X.tropicalis. RIP-seq, C Nelson Lau, Trey Toombs, Yuliya Sytnkova, Gungwei Chirn, Michael Blower We performed several replicates of a Piw CLIP-Seq experiment to isolate RNA fragments as CLIP-tags to discover which transcripts are preferentially bound by the Piwi protein. Then we performed several types of mRNA expression profiling experiments using several forms of mRNA-Seq library construction formats. Finally, we sequenced the piRNAs from the OSS cells 28031481 52877 SRP049739 piwil2 oocyte - adult CLIP-Seq adult oocyte Toombs JA et al. (2017) GSM1544070 CLIP-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/CLIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/CLIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/CLIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/CLIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/CLIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/CLIP-Seq/Readme.txt 63228 Nelson Lau Xenopus Piwi protein associated transcripts indicate regulation beyond transposons This study examines the population of transcripts associated with the Xenopus Piwi proteins, Xiwi and Xili, from X.laevis and X.tropicalis. RIP-seq, C Nelson Lau, Trey Toombs, Yuliya Sytnkova, Gungwei Chirn, Michael Blower We performed several replicates of a Piw CLIP-Seq experiment to isolate RNA fragments as CLIP-tags to discover which transcripts are preferentially bound by the Piwi protein. Then we performed several types of mRNA expression profiling experiments using several forms of mRNA-Seq library construction formats. Finally, we sequenced the piRNAs from the OSS cells 28031481 52877 SRP049739 piwil2 oocyte - adult RIP-Seq adult oocyte Toombs JA et al. (2017) GSM1544079 RIP-Seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/RIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/RIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/RIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/RIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/RIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/RIP-Seq/Readme.txt 63228 Nelson Lau Xenopus Piwi protein associated transcripts indicate regulation beyond transposons This study examines the population of transcripts associated with the Xenopus Piwi proteins, Xiwi and Xili, from X.laevis and X.tropicalis. RIP-seq, C Nelson Lau, Trey Toombs, Yuliya Sytnkova, Gungwei Chirn, Michael Blower We performed several replicates of a Piw CLIP-Seq experiment to isolate RNA fragments as CLIP-tags to discover which transcripts are preferentially bound by the Piwi protein. Then we performed several types of mRNA expression profiling experiments using several forms of mRNA-Seq library construction formats. Finally, we sequenced the piRNAs from the OSS cells 28031481 52877 SRP049739 oocyte - adult RNA-Seq adult oocyte Toombs JA et al. (2017) GSM1544080 RNA-Seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/RNA-Seq/Readme.txt 63228 Nelson Lau Xenopus Piwi protein associated transcripts indicate regulation beyond transposons This study examines the population of transcripts associated with the Xenopus Piwi proteins, Xiwi and Xili, from X.laevis and X.tropicalis. RIP-seq, C Nelson Lau, Trey Toombs, Yuliya Sytnkova, Gungwei Chirn, Michael Blower We performed several replicates of a Piw CLIP-Seq experiment to isolate RNA fragments as CLIP-tags to discover which transcripts are preferentially bound by the Piwi protein. Then we performed several types of mRNA expression profiling experiments using several forms of mRNA-Seq library construction formats. Finally, we sequenced the piRNAs from the OSS cells 28031481 52877 SRP049739 oocyte - oocyte V-VI RNA-Seq oocyte V oocyte Toombs JA et al. (2017) GSM1544075 RNA-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/RNA-Seq/Readme.txt 63228 Nelson Lau Xenopus Piwi protein associated transcripts indicate regulation beyond transposons This study examines the population of transcripts associated with the Xenopus Piwi proteins, Xiwi and Xili, from X.laevis and X.tropicalis. RIP-seq, C Nelson Lau, Trey Toombs, Yuliya Sytnkova, Gungwei Chirn, Michael Blower We performed several replicates of a Piw CLIP-Seq experiment to isolate RNA fragments as CLIP-tags to discover which transcripts are preferentially bound by the Piwi protein. Then we performed several types of mRNA expression profiling experiments using several forms of mRNA-Seq library construction formats. Finally, we sequenced the piRNAs from the OSS cells 28031481 52877 SRP049739 oocyte - oocyte III-IV RNA-Seq oocyte III oocyte Toombs JA et al. (2017) GSM1544074 RNA-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/RNA-Seq/Readme.txt 63228 Nelson Lau Xenopus Piwi protein associated transcripts indicate regulation beyond transposons This study examines the population of transcripts associated with the Xenopus Piwi proteins, Xiwi and Xili, from X.laevis and X.tropicalis. RIP-seq, C Nelson Lau, Trey Toombs, Yuliya Sytnkova, Gungwei Chirn, Michael Blower We performed several replicates of a Piw CLIP-Seq experiment to isolate RNA fragments as CLIP-tags to discover which transcripts are preferentially bound by the Piwi protein. Then we performed several types of mRNA expression profiling experiments using several forms of mRNA-Seq library construction formats. Finally, we sequenced the piRNAs from the OSS cells 28031481 52877 SRP049739 piwil1 oocyte - adult CLIP-Seq adult oocyte Toombs JA et al. (2017) GSM1544071,GSM1544072 CLIP-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/CLIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/CLIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/CLIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/CLIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/CLIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/CLIP-Seq/Readme.txt 63228 Nelson Lau Xenopus Piwi protein associated transcripts indicate regulation beyond transposons This study examines the population of transcripts associated with the Xenopus Piwi proteins, Xiwi and Xili, from X.laevis and X.tropicalis. RIP-seq, C Nelson Lau, Trey Toombs, Yuliya Sytnkova, Gungwei Chirn, Michael Blower We performed several replicates of a Piw CLIP-Seq experiment to isolate RNA fragments as CLIP-tags to discover which transcripts are preferentially bound by the Piwi protein. Then we performed several types of mRNA expression profiling experiments using several forms of mRNA-Seq library construction formats. Finally, we sequenced the piRNAs from the OSS cells 28031481 52877 SRP049739 piwil1 spermatid - adult CLIP-Seq adult spermatid Toombs JA et al. (2017) GSM1544073 CLIP-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/CLIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/CLIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/CLIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/CLIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/CLIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENTR_10.0/CLIP-Seq/Readme.txt 63228 Nelson Lau Xenopus Piwi protein associated transcripts indicate regulation beyond transposons This study examines the population of transcripts associated with the Xenopus Piwi proteins, Xiwi and Xili, from X.laevis and X.tropicalis. RIP-seq, C Nelson Lau, Trey Toombs, Yuliya Sytnkova, Gungwei Chirn, Michael Blower We performed several replicates of a Piw CLIP-Seq experiment to isolate RNA fragments as CLIP-tags to discover which transcripts are preferentially bound by the Piwi protein. Then we performed several types of mRNA expression profiling experiments using several forms of mRNA-Seq library construction formats. Finally, we sequenced the piRNAs from the OSS cells 28031481 52877 SRP049739 piwil2 oocyte - adult ncRNA-Seq adult oocyte Toombs JA et al. (2017) GSM1544077 ncRNA-Seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/ncRNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/ncRNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/ncRNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/ncRNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/ncRNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/ncRNA-Seq/Readme.txt 63228 Nelson Lau Xenopus Piwi protein associated transcripts indicate regulation beyond transposons This study examines the population of transcripts associated with the Xenopus Piwi proteins, Xiwi and Xili, from X.laevis and X.tropicalis. RIP-seq, C Nelson Lau, Trey Toombs, Yuliya Sytnkova, Gungwei Chirn, Michael Blower We performed several replicates of a Piw CLIP-Seq experiment to isolate RNA fragments as CLIP-tags to discover which transcripts are preferentially bound by the Piwi protein. Then we performed several types of mRNA expression profiling experiments using several forms of mRNA-Seq library construction formats. Finally, we sequenced the piRNAs from the OSS cells 28031481 52877 SRP049739 piwil1 oocyte - adult ncRNA-Seq adult oocyte Toombs JA et al. (2017) GSM1544076 ncRNA-Seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/ncRNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/ncRNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/ncRNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/ncRNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/ncRNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE63228/XENLA_10.1/ncRNA-Seq/Readme.txt 64551 Ian Quigley Occupancy and transcriptional profile of Prdm12 in posteriorized neural tissue V1 interneurons are a class of inhibitory neurons that play an essential role in vertebrate locomotion; however, the factors contributing to their spe Ian Quigley, Kristine Henningfeld, Chris Kintner, Eric Bellefroid, Claude Van Campenhout X. laevis embryos were injected with mRNAs encoding prdm12 constructs, along with the bmp inhibitor noggin. Presumptive ectoderm (neuralized by noggin) was dissected and treated with retinoic acid. Samples were then processed into RNAseq libraries or prdm12-FLAG was immunoprecipitated and its targets sequenced. Background was input prior to IP. 26443638 51355 SRP051597 animal cap + prdm12 - NF28 RNA-Seq NF28 animal cap Thélie A et al. (2015) GSM1574075,GSM1574076 Manipulations/mRNA Injection laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/Readme.txt 64551 Ian Quigley Occupancy and transcriptional profile of Prdm12 in posteriorized neural tissue V1 interneurons are a class of inhibitory neurons that play an essential role in vertebrate locomotion; however, the factors contributing to their spe Ian Quigley, Kristine Henningfeld, Chris Kintner, Eric Bellefroid, Claude Van Campenhout X. laevis embryos were injected with mRNAs encoding prdm12 constructs, along with the bmp inhibitor noggin. Presumptive ectoderm (neuralized by noggin) was dissected and treated with retinoic acid. Samples were then processed into RNAseq libraries or prdm12-FLAG was immunoprecipitated and its targets sequenced. Background was input prior to IP. 26443638 51355 SRP051597 animal cap + prdm12 - NF28 RNA-Seq NF28 animal cap Thélie A et al. (2015) GSM1574075,GSM1574076 RNA-Seq/Embryonic Tissues/Tailbud NF22 to NF44/animal cap laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/Readme.txt 64551 Ian Quigley Occupancy and transcriptional profile of Prdm12 in posteriorized neural tissue V1 interneurons are a class of inhibitory neurons that play an essential role in vertebrate locomotion; however, the factors contributing to their spe Ian Quigley, Kristine Henningfeld, Chris Kintner, Eric Bellefroid, Claude Van Campenhout X. laevis embryos were injected with mRNAs encoding prdm12 constructs, along with the bmp inhibitor noggin. Presumptive ectoderm (neuralized by noggin) was dissected and treated with retinoic acid. Samples were then processed into RNAseq libraries or prdm12-FLAG was immunoprecipitated and its targets sequenced. Background was input prior to IP. 26443638 51355 SRP051597 prdm12 animal cap + nog + RA - NF28 ChIP-Seq NF28 animal cap Thélie A et al. (2015) GSM1574082 ChIP-Seq/Transcription Factor/Prdm12 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/Readme.txt 64551 Ian Quigley Occupancy and transcriptional profile of Prdm12 in posteriorized neural tissue V1 interneurons are a class of inhibitory neurons that play an essential role in vertebrate locomotion; however, the factors contributing to their spe Ian Quigley, Kristine Henningfeld, Chris Kintner, Eric Bellefroid, Claude Van Campenhout X. laevis embryos were injected with mRNAs encoding prdm12 constructs, along with the bmp inhibitor noggin. Presumptive ectoderm (neuralized by noggin) was dissected and treated with retinoic acid. Samples were then processed into RNAseq libraries or prdm12-FLAG was immunoprecipitated and its targets sequenced. Background was input prior to IP. 26443638 51355 SRP051597 prdm12 animal cap + nog + RA - NF28 ChIP-Seq NF28 animal cap Thélie A et al. (2015) GSM1574082 Manipulations/Chemical laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/Readme.txt 64551 Ian Quigley Occupancy and transcriptional profile of Prdm12 in posteriorized neural tissue V1 interneurons are a class of inhibitory neurons that play an essential role in vertebrate locomotion; however, the factors contributing to their spe Ian Quigley, Kristine Henningfeld, Chris Kintner, Eric Bellefroid, Claude Van Campenhout X. laevis embryos were injected with mRNAs encoding prdm12 constructs, along with the bmp inhibitor noggin. Presumptive ectoderm (neuralized by noggin) was dissected and treated with retinoic acid. Samples were then processed into RNAseq libraries or prdm12-FLAG was immunoprecipitated and its targets sequenced. Background was input prior to IP. 26443638 51355 SRP051597 prdm12 animal cap + nog + RA - NF28 ChIP-Seq NF28 animal cap Thélie A et al. (2015) GSM1574082 Manipulations/mRNA Injection laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/Readme.txt 64551 Ian Quigley Occupancy and transcriptional profile of Prdm12 in posteriorized neural tissue V1 interneurons are a class of inhibitory neurons that play an essential role in vertebrate locomotion; however, the factors contributing to their spe Ian Quigley, Kristine Henningfeld, Chris Kintner, Eric Bellefroid, Claude Van Campenhout X. laevis embryos were injected with mRNAs encoding prdm12 constructs, along with the bmp inhibitor noggin. Presumptive ectoderm (neuralized by noggin) was dissected and treated with retinoic acid. Samples were then processed into RNAseq libraries or prdm12-FLAG was immunoprecipitated and its targets sequenced. Background was input prior to IP. 26443638 51355 SRP051597 prdm12 animal cap - NF28 ChIP-Seq NF28 animal cap Thélie A et al. (2015) GSM1574081 ChIP-Seq/Transcription Factor/Prdm12 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/Readme.txt 64551 Ian Quigley Occupancy and transcriptional profile of Prdm12 in posteriorized neural tissue V1 interneurons are a class of inhibitory neurons that play an essential role in vertebrate locomotion; however, the factors contributing to their spe Ian Quigley, Kristine Henningfeld, Chris Kintner, Eric Bellefroid, Claude Van Campenhout X. laevis embryos were injected with mRNAs encoding prdm12 constructs, along with the bmp inhibitor noggin. Presumptive ectoderm (neuralized by noggin) was dissected and treated with retinoic acid. Samples were then processed into RNAseq libraries or prdm12-FLAG was immunoprecipitated and its targets sequenced. Background was input prior to IP. 26443638 51355 SRP051597 prdm12 animal cap - NF28 ChIP-Seq NF28 animal cap Thélie A et al. (2015) GSM1574081 Manipulations/mRNA Injection laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/Readme.txt 64551 Ian Quigley Occupancy and transcriptional profile of Prdm12 in posteriorized neural tissue V1 interneurons are a class of inhibitory neurons that play an essential role in vertebrate locomotion; however, the factors contributing to their spe Ian Quigley, Kristine Henningfeld, Chris Kintner, Eric Bellefroid, Claude Van Campenhout X. laevis embryos were injected with mRNAs encoding prdm12 constructs, along with the bmp inhibitor noggin. Presumptive ectoderm (neuralized by noggin) was dissected and treated with retinoic acid. Samples were then processed into RNAseq libraries or prdm12-FLAG was immunoprecipitated and its targets sequenced. Background was input prior to IP. 26443638 51355 SRP051597 input animal cap - NF28 ChIP-Seq NF28 animal cap Thélie A et al. (2015) GSM1574083 None laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/Readme.txt 64551 Ian Quigley Occupancy and transcriptional profile of Prdm12 in posteriorized neural tissue V1 interneurons are a class of inhibitory neurons that play an essential role in vertebrate locomotion; however, the factors contributing to their spe Ian Quigley, Kristine Henningfeld, Chris Kintner, Eric Bellefroid, Claude Van Campenhout X. laevis embryos were injected with mRNAs encoding prdm12 constructs, along with the bmp inhibitor noggin. Presumptive ectoderm (neuralized by noggin) was dissected and treated with retinoic acid. Samples were then processed into RNAseq libraries or prdm12-FLAG was immunoprecipitated and its targets sequenced. Background was input prior to IP. 26443638 51355 SRP051597 animal cap + prdm12-VP16 - NF28 RNA-Seq NF28 animal cap Thélie A et al. (2015) GSM1574077,GSM1574078 Manipulations/mRNA Injection laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/Readme.txt 64551 Ian Quigley Occupancy and transcriptional profile of Prdm12 in posteriorized neural tissue V1 interneurons are a class of inhibitory neurons that play an essential role in vertebrate locomotion; however, the factors contributing to their spe Ian Quigley, Kristine Henningfeld, Chris Kintner, Eric Bellefroid, Claude Van Campenhout X. laevis embryos were injected with mRNAs encoding prdm12 constructs, along with the bmp inhibitor noggin. Presumptive ectoderm (neuralized by noggin) was dissected and treated with retinoic acid. Samples were then processed into RNAseq libraries or prdm12-FLAG was immunoprecipitated and its targets sequenced. Background was input prior to IP. 26443638 51355 SRP051597 animal cap + prdm12-VP16 - NF28 RNA-Seq NF28 animal cap Thélie A et al. (2015) GSM1574077,GSM1574078 RNA-Seq/Embryonic Tissues/Tailbud NF22 to NF44/animal cap laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/Readme.txt 64551 Ian Quigley Occupancy and transcriptional profile of Prdm12 in posteriorized neural tissue V1 interneurons are a class of inhibitory neurons that play an essential role in vertebrate locomotion; however, the factors contributing to their spe Ian Quigley, Kristine Henningfeld, Chris Kintner, Eric Bellefroid, Claude Van Campenhout X. laevis embryos were injected with mRNAs encoding prdm12 constructs, along with the bmp inhibitor noggin. Presumptive ectoderm (neuralized by noggin) was dissected and treated with retinoic acid. Samples were then processed into RNAseq libraries or prdm12-FLAG was immunoprecipitated and its targets sequenced. Background was input prior to IP. 26443638 51355 SRP051597 animal cap + nog - NF28 RNA-Seq NF28 animal cap Thélie A et al. (2015) GSM1574073,GSM1574074 Manipulations/mRNA Injection laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/Readme.txt 64551 Ian Quigley Occupancy and transcriptional profile of Prdm12 in posteriorized neural tissue V1 interneurons are a class of inhibitory neurons that play an essential role in vertebrate locomotion; however, the factors contributing to their spe Ian Quigley, Kristine Henningfeld, Chris Kintner, Eric Bellefroid, Claude Van Campenhout X. laevis embryos were injected with mRNAs encoding prdm12 constructs, along with the bmp inhibitor noggin. Presumptive ectoderm (neuralized by noggin) was dissected and treated with retinoic acid. Samples were then processed into RNAseq libraries or prdm12-FLAG was immunoprecipitated and its targets sequenced. Background was input prior to IP. 26443638 51355 SRP051597 animal cap + nog - NF28 RNA-Seq NF28 animal cap Thélie A et al. (2015) GSM1574073,GSM1574074 RNA-Seq/Embryonic Tissues/Tailbud NF22 to NF44/animal cap laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/Readme.txt 64551 Ian Quigley Occupancy and transcriptional profile of Prdm12 in posteriorized neural tissue V1 interneurons are a class of inhibitory neurons that play an essential role in vertebrate locomotion; however, the factors contributing to their spe Ian Quigley, Kristine Henningfeld, Chris Kintner, Eric Bellefroid, Claude Van Campenhout X. laevis embryos were injected with mRNAs encoding prdm12 constructs, along with the bmp inhibitor noggin. Presumptive ectoderm (neuralized by noggin) was dissected and treated with retinoic acid. Samples were then processed into RNAseq libraries or prdm12-FLAG was immunoprecipitated and its targets sequenced. Background was input prior to IP. 26443638 51355 SRP051597 animal cap - NF28 RNA-Seq NF28 animal cap Thélie A et al. (2015) GSM1574071,GSM1574072 RNA-Seq/Embryonic Tissues/Tailbud NF22 to NF44/animal cap laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/Readme.txt 64551 Ian Quigley Occupancy and transcriptional profile of Prdm12 in posteriorized neural tissue V1 interneurons are a class of inhibitory neurons that play an essential role in vertebrate locomotion; however, the factors contributing to their spe Ian Quigley, Kristine Henningfeld, Chris Kintner, Eric Bellefroid, Claude Van Campenhout X. laevis embryos were injected with mRNAs encoding prdm12 constructs, along with the bmp inhibitor noggin. Presumptive ectoderm (neuralized by noggin) was dissected and treated with retinoic acid. Samples were then processed into RNAseq libraries or prdm12-FLAG was immunoprecipitated and its targets sequenced. Background was input prior to IP. 26443638 51355 SRP051597 animal cap + EnR-prdm12 - NF28 RNA-Seq NF28 animal cap Thélie A et al. (2015) GSM1574079,GSM1574080 Manipulations/mRNA Injection laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/Readme.txt 64551 Ian Quigley Occupancy and transcriptional profile of Prdm12 in posteriorized neural tissue V1 interneurons are a class of inhibitory neurons that play an essential role in vertebrate locomotion; however, the factors contributing to their spe Ian Quigley, Kristine Henningfeld, Chris Kintner, Eric Bellefroid, Claude Van Campenhout X. laevis embryos were injected with mRNAs encoding prdm12 constructs, along with the bmp inhibitor noggin. Presumptive ectoderm (neuralized by noggin) was dissected and treated with retinoic acid. Samples were then processed into RNAseq libraries or prdm12-FLAG was immunoprecipitated and its targets sequenced. Background was input prior to IP. 26443638 51355 SRP051597 animal cap + EnR-prdm12 - NF28 RNA-Seq NF28 animal cap Thélie A et al. (2015) GSM1574079,GSM1574080 RNA-Seq/Embryonic Tissues/Tailbud NF22 to NF44/animal cap laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/RNA-Seq/Readme.txt 64551 Ian Quigley Occupancy and transcriptional profile of Prdm12 in posteriorized neural tissue V1 interneurons are a class of inhibitory neurons that play an essential role in vertebrate locomotion; however, the factors contributing to their spe Ian Quigley, Kristine Henningfeld, Chris Kintner, Eric Bellefroid, Claude Van Campenhout X. laevis embryos were injected with mRNAs encoding prdm12 constructs, along with the bmp inhibitor noggin. Presumptive ectoderm (neuralized by noggin) was dissected and treated with retinoic acid. Samples were then processed into RNAseq libraries or prdm12-FLAG was immunoprecipitated and its targets sequenced. Background was input prior to IP. 26443638 51355 SRP051597 input animal cap + nog + RA - NF28 ChIP-Seq NF28 animal cap Thélie A et al. (2015) GSM1574084 None laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE64551/XENLA_10.1/ChIP-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF32 (32hpf) - ClutchA RNA-Seq NF32 embryo Owens ND et al. (2016) GSM1606231 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF25 (21hpf) - ClutchA RNA-Seq NF25 embryo Owens ND et al. (2016) GSM1606217 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF28 (27hpf) - ClutchA RNA-Seq NF28 embryo Owens ND et al. (2016) GSM1606226 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF14 (14hpf) - ClutchA RNA-Seq NF14 embryo Owens ND et al. (2016) GSM1606203 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF41 (53hpf) - ClutchA RNA-Seq NF41 embryo Owens ND et al. (2016) GSM1606251 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF5 (2hpf) - ClutchA RNA-Seq NF5 embryo Owens ND et al. (2016) GSM1606179 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF10 (6.5hpf) - ClutchA RNA-Seq NF10 embryo Owens ND et al. (2016) GSM1606188 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF39 (44hpf) - ClutchA RNA-Seq NF39 embryo Owens ND et al. (2016) GSM1606242 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF7 (3.5hpf) - ClutchA RNA-Seq NF7 embryo Owens ND et al. (2016) GSM1606182 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF22 (17.5hpf) - ClutchA RNA-Seq NF22 embryo Owens ND et al. (2016) GSM1606210 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF40 (50hpf) - ClutchA RNA-Seq NF40 embryo Owens ND et al. (2016) GSM1606248 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF1 (0hpf) - ClutchA RNA-Seq NF1 embryo Owens ND et al. (2016) GSM1606175 RNA-Seq/Embryonic Tissues/fertilized egg tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF12 (10hpf) - ClutchA rd RNA-Seq NF12 embryo Owens ND et al. (2016) GSM1606283 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF24 (20hpf) - ClutchA rd RNA-Seq NF24 embryo Owens ND et al. (2016) GSM1606305 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF16-17 (15hpf) - ClutchA rd RNA-Seq NF16 embryo Owens ND et al. (2016) GSM1606294 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF21 (16.5hpf) - ClutchA rd RNA-Seq NF21 embryo Owens ND et al. (2016) GSM1606298 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF9 (6hpf) - ClutchA rd RNA-Seq NF9 embryo Owens ND et al. (2016) GSM1606275 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF10 (7.5hpf) - ClutchA rd RNA-Seq NF10 embryo Owens ND et al. (2016) GSM1606278 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF16-17 (15hpf) - ClutchA RNA-Seq NF16 embryo Owens ND et al. (2016) GSM1606205 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF35/36 (37hpf) - ClutchA RNA-Seq NF35/36 embryo Owens ND et al. (2016) GSM1606236 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF13 (12.5hpf) - ClutchA RNA-Seq NF13 embryo Owens ND et al. (2016) GSM1606200 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF5 (2hpf) - ClutchA rd RNA-Seq NF5 embryo Owens ND et al. (2016) GSM1606306 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF22 (17.5hpf) - ClutchA rd RNA-Seq NF22 embryo Owens ND et al. (2016) GSM1606300 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF9 (5hpf) - ClutchA rd RNA-Seq NF9 embryo Owens ND et al. (2016) GSM1606272 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF25 (21.5hpf) - ClutchA RNA-Seq NF25 embryo Owens ND et al. (2016) GSM1606218,GSM1606266 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF12 (9hpf) - ClutchA rd RNA-Seq NF12 embryo Owens ND et al. (2016) GSM1606281 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF7 (3.5hpf) - ClutchA rd RNA-Seq NF7 embryo Owens ND et al. (2016) GSM1606316 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF37/38 (40hpf) - ClutchA RNA-Seq NF37/38 embryo Owens ND et al. (2016) GSM1606239 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF40 (49hpf) - ClutchA RNA-Seq NF40 embryo Owens ND et al. (2016) GSM1606247 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF12.5 (10.5hpf) - ClutchA RNA-Seq NF12.5 embryo Owens ND et al. (2016) GSM1606196 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF3 (1.5hpf) - ClutchA RNA-Seq NF3 embryo Owens ND et al. (2016) GSM1606178 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF33/34 (35hpf) - ClutchA RNA-Seq NF33/34 embryo Owens ND et al. (2016) GSM1606234 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF13 (13hpf) - ClutchA rd RNA-Seq NF13 embryo Owens ND et al. (2016) GSM1606290 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF24 (19hpf) - ClutchA rd RNA-Seq NF24 embryo Owens ND et al. (2016) GSM1606303 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF1 (0.5hpf) - ClutchA RNA-Seq NF1 embryo Owens ND et al. (2016) GSM1606176 RNA-Seq/Whole Embryo/fertilized egg tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF20 (16hpf) - ClutchA rd RNA-Seq NF20 embryo Owens ND et al. (2016) GSM1606297 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF10 (7hpf) - ClutchA rd RNA-Seq NF10 embryo Owens ND et al. (2016) GSM1606277 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF26 (22.5hpf) - ClutchA RNA-Seq NF26 embryo Owens ND et al. (2016) GSM1606220 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF9 (6hpf) - ClutchA RNA-Seq NF9 embryo Owens ND et al. (2016) GSM1606187 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF11 (8hpf) - ClutchA RNA-Seq NF11 embryo Owens ND et al. (2016) GSM1606191 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF42 (59hpf) - ClutchA RNA-Seq NF42 embryo Owens ND et al. (2016) GSM1606257 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF24 (19.5hpf) - ClutchA RNA-Seq NF24 embryo Owens ND et al. (2016) GSM1606214 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF10 (7hpf) - ClutchA RNA-Seq NF10 embryo Owens ND et al. (2016) GSM1606189 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF42 (61hpf) - ClutchA RNA-Seq NF42 embryo Owens ND et al. (2016) GSM1606259 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF43 (66hpf) - ClutchA RNA-Seq NF43 embryo Owens ND et al. (2016) GSM1606264 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF27 (26hpf) - ClutchA RNA-Seq NF27 embryo Owens ND et al. (2016) GSM1606225 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF26 (23.5hpf) - ClutchA RNA-Seq NF26 embryo Owens ND et al. (2016) GSM1606222 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF1 (0.5hpf) - ClutchA rd RNA-Seq NF1 embryo Owens ND et al. (2016) GSM1606273 RNA-Seq/Whole Embryo/fertilized egg tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF10 (6.5hpf) - ClutchA rd RNA-Seq NF10 embryo Owens ND et al. (2016) GSM1606276 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF10 (7.5hpf) - ClutchA RNA-Seq NF10 embryo Owens ND et al. (2016) GSM1606190 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF11 (8hpf) - ClutchA rd RNA-Seq NF11 embryo Owens ND et al. (2016) GSM1606279 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF12 (8.5hpf) - ClutchA rd RNA-Seq NF12 embryo Owens ND et al. (2016) GSM1606280 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF12 (9.5hpf) - ClutchA rd RNA-Seq NF12 embryo Owens ND et al. (2016) GSM1606282 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF12 (10hpf) - ClutchA RNA-Seq NF12 embryo Owens ND et al. (2016) GSM1606195 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF12 (8.5hpf) - ClutchA RNA-Seq NF12 embryo Owens ND et al. (2016) GSM1606192 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF12 (9hpf) - ClutchA RNA-Seq NF12 embryo Owens ND et al. (2016) GSM1606193 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF12 (9.5hpf) - ClutchA RNA-Seq NF12 embryo Owens ND et al. (2016) GSM1606194 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF12.5 (10.5hpf) - ClutchA rd RNA-Seq NF12.5 embryo Owens ND et al. (2016) GSM1606285 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF12.5 (11hpf) - ClutchA rd RNA-Seq NF12.5 embryo Owens ND et al. (2016) GSM1606286 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF12.5 (11.5hpf) - ClutchA rd RNA-Seq NF12.5 embryo Owens ND et al. (2016) GSM1606287 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF12.5 (11hpf) - ClutchA RNA-Seq NF12.5 embryo Owens ND et al. (2016) GSM1606197 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF12.5 (11.5hpf) - ClutchA RNA-Seq NF12.5 embryo Owens ND et al. (2016) GSM1606198,GSM1606265 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF14 (13.5hpf) - ClutchA rd RNA-Seq NF14 embryo Owens ND et al. (2016) GSM1606291 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF15 (14.5hpf) - ClutchA rd RNA-Seq NF15 embryo Owens ND et al. (2016) GSM1606293 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF15 (14.5hpf) - ClutchA RNA-Seq NF15 embryo Owens ND et al. (2016) GSM1606204 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF20 (16hpf) - ClutchA RNA-Seq NF20 embryo Owens ND et al. (2016) GSM1606207 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF21 (17hpf) - ClutchA rd RNA-Seq NF21 embryo Owens ND et al. (2016) GSM1606299 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF21 (16.5hpf) - ClutchA RNA-Seq NF21 embryo Owens ND et al. (2016) GSM1606208 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF21 (17hpf) - ClutchA RNA-Seq NF21 embryo Owens ND et al. (2016) GSM1606209 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF22 (18hpf) - ClutchA RNA-Seq NF22 embryo Owens ND et al. (2016) GSM1606211 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF23 (18.5hpf) - ClutchA rd RNA-Seq NF23 embryo Owens ND et al. (2016) GSM1606302 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF24 (19.5hpf) - ClutchA rd RNA-Seq NF24 embryo Owens ND et al. (2016) GSM1606304 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF24 (20hpf) - ClutchA RNA-Seq NF24 embryo Owens ND et al. (2016) GSM1606215 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF24 (20.5hpf) - ClutchA RNA-Seq NF24 embryo Owens ND et al. (2016) GSM1606216 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF25 (21hpf) - ClutchA rd RNA-Seq NF25 embryo Owens ND et al. (2016) GSM1606308 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF25 (21.5hpf) - ClutchA rd RNA-Seq NF25 embryo Owens ND et al. (2016) GSM1606309 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF25 (22hpf) - ClutchA rd RNA-Seq NF25 embryo Owens ND et al. (2016) GSM1606310 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF25 (22hpf) - ClutchA RNA-Seq NF25 embryo Owens ND et al. (2016) GSM1606219 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF26 (22.5hpf) - ClutchA rd RNA-Seq NF26 embryo Owens ND et al. (2016) GSM1606311 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF26 (23.5hpf) - ClutchA rd RNA-Seq NF26 embryo Owens ND et al. (2016) GSM1606313 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF26 (23hpf) - ClutchA RNA-Seq NF26 embryo Owens ND et al. (2016) GSM1606221 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF27 (24hpf) - ClutchA RNA-Seq NF27 embryo Owens ND et al. (2016) GSM1606223 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF27 (25hpf) - ClutchA RNA-Seq NF27 embryo Owens ND et al. (2016) GSM1606224 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF28 (28hpf) - ClutchA RNA-Seq NF28 embryo Owens ND et al. (2016) GSM1606227 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF29/30 (29hpf) - ClutchA RNA-Seq NF29/30 embryo Owens ND et al. (2016) GSM1606228 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF3 (1.5hpf) - ClutchA rd RNA-Seq NF3 embryo Owens ND et al. (2016) GSM1606295 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF31 (30hpf) - ClutchA RNA-Seq NF31 embryo Owens ND et al. (2016) GSM1606229,GSM1606267 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF32 (31hpf) - ClutchA RNA-Seq NF32 embryo Owens ND et al. (2016) GSM1606230 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF33/34 (33hpf) - ClutchA RNA-Seq NF33/34 embryo Owens ND et al. (2016) GSM1606232,GSM1606268 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF33/34 (34hpf) - ClutchA RNA-Seq NF33/34 embryo Owens ND et al. (2016) GSM1606233 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF35/36 (36hpf) - ClutchA RNA-Seq NF35/36 embryo Owens ND et al. (2016) GSM1606235 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF37/38 (38hpf) - ClutchA RNA-Seq NF37/38 embryo Owens ND et al. (2016) GSM1606237 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF37/38 (39hpf) - ClutchA RNA-Seq NF37/38 embryo Owens ND et al. (2016) GSM1606238 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF39 (41hpf) - ClutchA RNA-Seq NF39 embryo Owens ND et al. (2016) GSM1606240 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF39 (42hpf) - ClutchA RNA-Seq NF39 embryo Owens ND et al. (2016) GSM1606241 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF39 (45hpf) - ClutchA RNA-Seq NF39 embryo Owens ND et al. (2016) GSM1606243 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF40 (47hpf) - ClutchA RNA-Seq NF40 embryo Owens ND et al. (2016) GSM1606245 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF40 (48hpf) - ClutchA RNA-Seq NF40 embryo Owens ND et al. (2016) GSM1606246 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF41 (51hpf) - ClutchA RNA-Seq NF41 embryo Owens ND et al. (2016) GSM1606249 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF41 (52hpf) - ClutchA RNA-Seq NF41 embryo Owens ND et al. (2016) GSM1606250,GSM1606269 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF41 (54hpf) - ClutchA RNA-Seq NF41 embryo Owens ND et al. (2016) GSM1606252 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF41 (55hpf) - ClutchA RNA-Seq NF41 embryo Owens ND et al. (2016) GSM1606253 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF42 (57hpf) - ClutchA RNA-Seq NF42 embryo Owens ND et al. (2016) GSM1606255 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF42 (58hpf) - ClutchA RNA-Seq NF42 embryo Owens ND et al. (2016) GSM1606256 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF42 (60hpf) - ClutchA RNA-Seq NF42 embryo Owens ND et al. (2016) GSM1606258 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF42 (62hpf) - ClutchA RNA-Seq NF42 embryo Owens ND et al. (2016) GSM1606260 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF43 (64hpf) - ClutchA RNA-Seq NF43 embryo Owens ND et al. (2016) GSM1606262,GSM1606270 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF6 (2.5hpf) - ClutchA RNA-Seq NF6 embryo Owens ND et al. (2016) GSM1606180 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF7 (3hpf) - ClutchA rd RNA-Seq NF7 embryo Owens ND et al. (2016) GSM1606315 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF7 (3hpf) - ClutchA RNA-Seq NF7 embryo Owens ND et al. (2016) GSM1606181 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF8 (4hpf) - ClutchA RNA-Seq NF8 embryo Owens ND et al. (2016) GSM1606183 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF9 (4.5hpf) - ClutchA rd RNA-Seq NF9 embryo Owens ND et al. (2016) GSM1606318 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF9 (5.5hpf) - ClutchA rd RNA-Seq NF9 embryo Owens ND et al. (2016) GSM1606274 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF9 (4.5hpf) - ClutchA RNA-Seq NF9 embryo Owens ND et al. (2016) GSM1606184 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF9 (5hpf) - ClutchA RNA-Seq NF9 embryo Owens ND et al. (2016) GSM1606185 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF1 (0hpf) - ClutchA rd RNA-Seq NF1 embryo Owens ND et al. (2016) GSM1606271 RNA-Seq/Embryonic Tissues/fertilized egg tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF43 (65hpf) - ClutchA RNA-Seq NF43 embryo Owens ND et al. (2016) GSM1606263 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF22 (18hpf) - ClutchA rd RNA-Seq NF22 embryo Owens ND et al. (2016) GSM1606301 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF13 (12hpf) - ClutchA RNA-Seq NF13 embryo Owens ND et al. (2016) GSM1606199 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF14 (14hpf) - ClutchA rd RNA-Seq NF14 embryo Owens ND et al. (2016) GSM1606292 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF42 (56hpf) - ClutchA RNA-Seq NF42 embryo Owens ND et al. (2016) GSM1606254 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF24 (20.5hpf) - ClutchA rd RNA-Seq NF24 embryo Owens ND et al. (2016) GSM1606307 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF13 (12.5hpf) - ClutchA rd RNA-Seq NF13 embryo Owens ND et al. (2016) GSM1606289 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF18-19 (15.5hpf) - ClutchA RNA-Seq NF18 embryo Owens ND et al. (2016) GSM1606206 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF6 (2.5hpf) - ClutchA rd RNA-Seq NF6 embryo Owens ND et al. (2016) GSM1606314 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF1 (0.5hpf) - ClutchB RNA-Seq NF1 embryo Owens ND et al. (2016) GSM1606320 RNA-Seq/Whole Embryo/fertilized egg tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF1 (0hpf) - ClutchB RNA-Seq NF1 embryo Owens ND et al. (2016) GSM1606319 RNA-Seq/Embryonic Tissues/fertilized egg tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF12.5 (10.5hpf) - ClutchB RNA-Seq NF12.5 embryo Owens ND et al. (2016) GSM1606340 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF12 (10hpf) - ClutchB RNA-Seq NF12 embryo Owens ND et al. (2016) GSM1606339 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF12.5 (11.5hpf) - ClutchB RNA-Seq NF12.5 embryo Owens ND et al. (2016) GSM1606342 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF13 (12.5hpf) - ClutchB RNA-Seq NF13 embryo Owens ND et al. (2016) GSM1606344 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF13 (12hpf) - ClutchB RNA-Seq NF13 embryo Owens ND et al. (2016) GSM1606343 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF13 (13hpf) - ClutchB RNA-Seq NF13 embryo Owens ND et al. (2016) GSM1606345 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF15 (14.5hpf) - ClutchB RNA-Seq NF15 embryo Owens ND et al. (2016) GSM1606348 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF14 (14hpf) - ClutchB RNA-Seq NF14 embryo Owens ND et al. (2016) GSM1606347 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF16-17 (15hpf) - ClutchB RNA-Seq NF16 embryo Owens ND et al. (2016) GSM1606349 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF21 (16.5hpf) - ClutchB RNA-Seq NF21 embryo Owens ND et al. (2016) GSM1606352 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF20 (16hpf) - ClutchB RNA-Seq NF20 embryo Owens ND et al. (2016) GSM1606351 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF21 (17hpf) - ClutchB RNA-Seq NF21 embryo Owens ND et al. (2016) GSM1606353 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF23 (18.5hpf) - ClutchB RNA-Seq NF23 embryo Owens ND et al. (2016) GSM1606356 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF24 (19.5hpf) - ClutchB RNA-Seq NF24 embryo Owens ND et al. (2016) GSM1606358 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF24 (19hpf) - ClutchB RNA-Seq NF24 embryo Owens ND et al. (2016) GSM1606357 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF2- (1hpf) - ClutchB RNA-Seq NF2- embryo Owens ND et al. (2016) GSM1606321 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF24 (20.5hpf) - ClutchB RNA-Seq NF24 embryo Owens ND et al. (2016) GSM1606360 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF24 (20hpf) - ClutchB RNA-Seq NF24 embryo Owens ND et al. (2016) GSM1606359 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF25 (21.5hpf) - ClutchB RNA-Seq NF25 embryo Owens ND et al. (2016) GSM1606362 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF26 (23.5hpf) - ClutchB RNA-Seq NF26 embryo Owens ND et al. (2016) GSM1606366 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF27 (24hpf) - ClutchB RNA-Seq NF27 embryo Owens ND et al. (2016) GSM1606367 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF7 (3.5hpf) - ClutchB RNA-Seq NF7 embryo Owens ND et al. (2016) GSM1606326 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF7 (3hpf) - ClutchB RNA-Seq NF7 embryo Owens ND et al. (2016) GSM1606325 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF9 (4.5hpf) - ClutchB RNA-Seq NF9 embryo Owens ND et al. (2016) GSM1606328 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF8 (4hpf) - ClutchB RNA-Seq NF8 embryo Owens ND et al. (2016) GSM1606327 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF9 (5.5hpf) - ClutchB RNA-Seq NF9 embryo Owens ND et al. (2016) GSM1606330 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF9 (5hpf) - ClutchB RNA-Seq NF9 embryo Owens ND et al. (2016) GSM1606329 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF10 (6.5hpf) - ClutchB RNA-Seq NF10 embryo Owens ND et al. (2016) GSM1606332 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF9 (6hpf) - ClutchB RNA-Seq NF9 embryo Owens ND et al. (2016) GSM1606331 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF12 (9hpf) - ClutchB RNA-Seq NF12 embryo Owens ND et al. (2016) GSM1606337 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF12 (9.5hpf) - ClutchB RNA-Seq NF12 embryo Owens ND et al. (2016) GSM1606338 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF12 (8.5hpf) - ClutchB RNA-Seq NF12 embryo Owens ND et al. (2016) GSM1606336 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF10 (7.5hpf) - ClutchB RNA-Seq NF10 embryo Owens ND et al. (2016) GSM1606334 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF10 (7hpf) - ClutchB RNA-Seq NF10 embryo Owens ND et al. (2016) GSM1606333 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF11 (8hpf) - ClutchB RNA-Seq NF11 embryo Owens ND et al. (2016) GSM1606335 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF13 (13hpf) - ClutchA RNA-Seq NF13 embryo Owens ND et al. (2016) GSM1606201 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF14 (13.5hpf) - ClutchA RNA-Seq NF14 embryo Owens ND et al. (2016) GSM1606202 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF18-19 (15.5hpf) - ClutchA rd RNA-Seq NF18 embryo Owens ND et al. (2016) GSM1606296 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF2- (1hpf) - ClutchA rd RNA-Seq NF2- embryo Owens ND et al. (2016) GSM1606284 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF2- (1hpf) - ClutchA RNA-Seq NF2- embryo Owens ND et al. (2016) GSM1606177 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF23 (18.5hpf) - ClutchA RNA-Seq NF23 embryo Owens ND et al. (2016) GSM1606212 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF24 (19hpf) - ClutchA RNA-Seq NF24 embryo Owens ND et al. (2016) GSM1606213 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF26 (23hpf) - ClutchA rd RNA-Seq NF26 embryo Owens ND et al. (2016) GSM1606312 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF40 (46hpf) - ClutchA RNA-Seq NF40 embryo Owens ND et al. (2016) GSM1606244 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF43 (63hpf) - ClutchA RNA-Seq NF43 embryo Owens ND et al. (2016) GSM1606261 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF8 (4hpf) - ClutchA rd RNA-Seq NF8 embryo Owens ND et al. (2016) GSM1606317 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF9 (5.5hpf) - ClutchA RNA-Seq NF9 embryo Owens ND et al. (2016) GSM1606186 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF25 (21hpf) - ClutchB RNA-Seq NF25 embryo Owens ND et al. (2016) GSM1606361 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF26 (22.5hpf) - ClutchB RNA-Seq NF26 embryo Owens ND et al. (2016) GSM1606364 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF25 (22hpf) - ClutchB RNA-Seq NF25 embryo Owens ND et al. (2016) GSM1606363 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF26 (23hpf) - ClutchB RNA-Seq NF26 embryo Owens ND et al. (2016) GSM1606365 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF5 (2hpf) - ClutchB RNA-Seq NF5 embryo Owens ND et al. (2016) GSM1606323 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF3 (1.5hpf) - ClutchB RNA-Seq NF3 embryo Owens ND et al. (2016) GSM1606322 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF12.5 (11hpf) - ClutchB RNA-Seq NF12.5 embryo Owens ND et al. (2016) GSM1606341 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF13 (12hpf) - ClutchA rd RNA-Seq NF13 embryo Owens ND et al. (2016) GSM1606288 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF14 (13.5hpf) - ClutchB RNA-Seq NF14 embryo Owens ND et al. (2016) GSM1606346 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF18-19 (15.5hpf) - ClutchB RNA-Seq NF18 embryo Owens ND et al. (2016) GSM1606350 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF22 (17.5hpf) - ClutchB RNA-Seq NF22 embryo Owens ND et al. (2016) GSM1606354 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF22 (18hpf) - ClutchB RNA-Seq NF22 embryo Owens ND et al. (2016) GSM1606355 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 65785 Mike Gilchrist Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing. 26774488 51804 SRP053406 WE - NF6 (2.5hpf) - ClutchB RNA-Seq NF6 embryo Owens ND et al. (2016) GSM1606324 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE65785/XENTR_10.0/RNA-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K9ac WE - NF10.5 ChIP-Seq NF10.5 embryo Hontelez S et al. (2015) GSM1659911 ChIP-Seq/Epigenetic/H3K9ac tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 Pol II WE - NF9 ChIP-Seq NF9 embryo Hontelez S et al. (2015) GSM1659927 ChIP-Seq/Transcription Factor/Pol II tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K36me3 WE - NF16 ChIP-Seq NF16 embryo Hontelez S et al. (2015) GSM1659918 ChIP-Seq/Epigenetic/H3K36me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K4me3 WE - NF16 ChIP-Seq NF16 embryo Hontelez S et al. (2015) GSM1659907 ChIP-Seq/Epigenetic/H3K4me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K4me3 WE - NF9 ChIP-Seq NF9 embryo Hontelez S et al. (2015) GSM1659902 ChIP-Seq/Epigenetic/H3K4me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 WE + alpha amanitin - NF11 RNA-Seq NF11 embryo Hontelez S et al. (2015) GSM1974231 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/RNA-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 WE + alpha amanitin - NF11 RNA-Seq NF11 embryo Hontelez S et al. (2015) GSM1974231 Manipulations/Chemical tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/RNA-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K36me3 WE - NF10.5 ChIP-Seq NF10.5 embryo Hontelez S et al. (2015) GSM1659916 ChIP-Seq/Epigenetic/H3K36me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K9me2 WE - NF29/30 ChIP-Seq NF29/30 embryo Hontelez S et al. (2015) GSM1659944 ChIP-Seq/Epigenetic/H3K9me2 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K9me2 WE - NF12 ChIP-Seq NF12 embryo Hontelez S et al. (2015) GSM1659942 ChIP-Seq/Epigenetic/H3K9me2 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K27me3 WE + alpha amanitin - NF11 ChIP-Seq NF11 embryo Hontelez S et al. (2015) GSM1659935,GSM1974225 ChIP-Seq/Epigenetic/H3K27me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K27me3 WE + alpha amanitin - NF11 ChIP-Seq NF11 embryo Hontelez S et al. (2015) GSM1659935,GSM1974225 Manipulations/Chemical tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K4me3 WE - NF29/30 ChIP-Seq NF29/30 embryo Hontelez S et al. (2015) GSM1659908 ChIP-Seq/Epigenetic/H3K4me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K9me3 WE - NF29/30 ChIP-Seq NF29/30 embryo Hontelez S et al. (2015) GSM1659949 ChIP-Seq/Epigenetic/H3K9me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 WE - NF11 RNA-Seq NF11 embryo Hontelez S et al. (2015) GSM1974232 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/RNA-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 Pol II WE - NF16 ChIP-Seq NF16 embryo Hontelez S et al. (2015) GSM1659930 ChIP-Seq/Transcription Factor/Pol II tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 ep300 WE - NF29/30 ChIP-Seq NF29/30 embryo Hontelez S et al. (2015) GSM1659926 ChIP-Seq/Transcription Factor/ep300 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K4me3 WE - NF8 ChIP-Seq NF8 embryo Hontelez S et al. (2015) GSM1659901 ChIP-Seq/Epigenetic/H3K4me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K27me3 WE - NF11 ChIP-Seq NF11 embryo Hontelez S et al. (2015) GSM1659936,GSM1974226 ChIP-Seq/Epigenetic/H3K27me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K9me3 WE - NF9 ChIP-Seq NF9 embryo Hontelez S et al. (2015) GSM1659945 ChIP-Seq/Epigenetic/H3K9me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K9ac WE - NF16 ChIP-Seq NF16 embryo Hontelez S et al. (2015) GSM1659913 ChIP-Seq/Epigenetic/H3K9ac tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 ep300 WE - NF11 ChIP-Seq NF11 embryo Hontelez S et al. (2015) GSM1659923,GSM1974228 ChIP-Seq/Transcription Factor/ep300 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K4me3 WE - NF12 ChIP-Seq NF12 embryo Hontelez S et al. (2015) GSM1659906 ChIP-Seq/Epigenetic/H3K4me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H4K20me3 WE - NF9 ChIP-Seq NF9 embryo Hontelez S et al. (2015) GSM1659950 ChIP-Seq/Epigenetic/H4K20me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 Pol II WE - NF12 ChIP-Seq NF12 embryo Hontelez S et al. (2015) GSM1659929 ChIP-Seq/Transcription Factor/Pol II tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K27me3 WE - NF9 ChIP-Seq NF9 embryo Hontelez S et al. (2015) GSM1659933 ChIP-Seq/Epigenetic/H3K27me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K9me3 WE - NF16 ChIP-Seq NF16 embryo Hontelez S et al. (2015) GSM1659948 ChIP-Seq/Epigenetic/H3K9me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K9ac WE - NF9 ChIP-Seq NF9 embryo Hontelez S et al. (2015) GSM1659910 ChIP-Seq/Epigenetic/H3K9ac tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K27me3 WE - NF10.5 ChIP-Seq NF10.5 embryo Hontelez S et al. (2015) GSM1659934 ChIP-Seq/Epigenetic/H3K27me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K9me3 WE - NF12 ChIP-Seq NF12 embryo Hontelez S et al. (2015) GSM1659947 ChIP-Seq/Epigenetic/H3K9me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 Pol II WE - NF29/30 ChIP-Seq NF29/30 embryo Hontelez S et al. (2015) GSM1659931 ChIP-Seq/Transcription Factor/Pol II tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H4K20me3 WE - NF10.5 ChIP-Seq NF10.5 embryo Hontelez S et al. (2015) GSM1659951 ChIP-Seq/Epigenetic/H4K20me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 Pol II WE - NF10.5 ChIP-Seq NF10.5 embryo Hontelez S et al. (2015) GSM1659928 ChIP-Seq/Transcription Factor/Pol II tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 WE - NF10.5 Bisulfite-Seq NF10.5 embryo Hontelez S et al. (2015) GSM1677167 Bisulfite-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/Bisulfite-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/Bisulfite-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/Bisulfite-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/Bisulfite-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/Bisulfite-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/Bisulfite-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K9me3 WE - NF10.5 ChIP-Seq NF10.5 embryo Hontelez S et al. (2015) GSM1659946 ChIP-Seq/Epigenetic/H3K9me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K4me3 WE - NF10.5 ChIP-Seq NF10.5 embryo Hontelez S et al. (2015) GSM1659903 ChIP-Seq/Epigenetic/H3K4me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 ep300 WE - NF10.5 ChIP-Seq NF10.5 embryo Hontelez S et al. (2015) GSM1659921 ChIP-Seq/Transcription Factor/ep300 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K9me2 WE - NF10.5 ChIP-Seq NF10.5 embryo Hontelez S et al. (2015) GSM1659941 ChIP-Seq/Epigenetic/H3K9me2 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K4me1 WE - NF10.5 ChIP-Seq NF10.5 embryo Hontelez S et al. (2015) GSM1659897 ChIP-Seq/Epigenetic/H3K4me1 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K4me3 WE + alpha amanitin - NF11 ChIP-Seq NF11 embryo Hontelez S et al. (2015) GSM1659904,GSM1974223 ChIP-Seq/Epigenetic/H3K4me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K4me3 WE + alpha amanitin - NF11 ChIP-Seq NF11 embryo Hontelez S et al. (2015) GSM1659904,GSM1974223 Manipulations/Chemical tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K4me3 WE - NF11 ChIP-Seq NF11 embryo Hontelez S et al. (2015) GSM1659905,GSM1974224 ChIP-Seq/Epigenetic/H3K4me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 ep300 WE + alpha amanitin - NF11 ChIP-Seq NF11 embryo Hontelez S et al. (2015) GSM1659922,GSM1974227 ChIP-Seq/Transcription Factor/ep300 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 ep300 WE + alpha amanitin - NF11 ChIP-Seq NF11 embryo Hontelez S et al. (2015) GSM1659922,GSM1974227 Manipulations/Chemical tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 Pol II WE - NF11 ChIP-Seq NF11 embryo Hontelez S et al. (2015) GSM1974230 ChIP-Seq/Transcription Factor/Pol II tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 Pol II WE + alpha amanitin - NF11 ChIP-Seq NF11 embryo Hontelez S et al. (2015) GSM1974229 ChIP-Seq/Transcription Factor/Pol II tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 Pol II WE + alpha amanitin - NF11 ChIP-Seq NF11 embryo Hontelez S et al. (2015) GSM1974229 Manipulations/Chemical tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K27me3 WE - NF12 ChIP-Seq NF12 embryo Hontelez S et al. (2015) GSM1659937 ChIP-Seq/Epigenetic/H3K27me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K36me3 WE - NF12 ChIP-Seq NF12 embryo Hontelez S et al. (2015) GSM1659917 ChIP-Seq/Epigenetic/H3K36me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H4K20me3 WE - NF12 ChIP-Seq NF12 embryo Hontelez S et al. (2015) GSM1659952 ChIP-Seq/Epigenetic/H4K20me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 ep300 WE - NF12 ChIP-Seq NF12 embryo Hontelez S et al. (2015) GSM1659924 ChIP-Seq/Transcription Factor/ep300 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K9ac WE - NF12 ChIP-Seq NF12 embryo Hontelez S et al. (2015) GSM1659912 ChIP-Seq/Epigenetic/H3K9ac tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K4me1 WE - NF12 ChIP-Seq NF12 embryo Hontelez S et al. (2015) GSM1659898 ChIP-Seq/Epigenetic/H3K4me1 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K27me3 WE - NF16 ChIP-Seq NF16 embryo Hontelez S et al. (2015) GSM1659938 ChIP-Seq/Epigenetic/H3K27me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H4K20me3 WE - NF16 ChIP-Seq NF16 embryo Hontelez S et al. (2015) GSM1659953 ChIP-Seq/Epigenetic/H4K20me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 ep300 WE - NF16 ChIP-Seq NF16 embryo Hontelez S et al. (2015) GSM1659925 ChIP-Seq/Transcription Factor/ep300 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K9me2 WE - NF16 ChIP-Seq NF16 embryo Hontelez S et al. (2015) GSM1659943 ChIP-Seq/Epigenetic/H3K9me2 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K4me1 WE - NF16 ChIP-Seq NF16 embryo Hontelez S et al. (2015) GSM1659899 ChIP-Seq/Epigenetic/H3K4me1 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 input WE - NF29/30 ChIP-Seq NF29/30 embryo Hontelez S et al. (2015) GSM1659955 None tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K27me3 WE - NF29/30 ChIP-Seq NF29/30 embryo Hontelez S et al. (2015) GSM1659939 ChIP-Seq/Epigenetic/H3K27me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K36me3 WE - NF29/30 ChIP-Seq NF29/30 embryo Hontelez S et al. (2015) GSM1659919 ChIP-Seq/Epigenetic/H3K36me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H4K20me3 WE - NF29/30 ChIP-Seq NF29/30 embryo Hontelez S et al. (2015) GSM1659954 ChIP-Seq/Epigenetic/H4K20me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K9ac WE - NF29/30 ChIP-Seq NF29/30 embryo Hontelez S et al. (2015) GSM1659914 ChIP-Seq/Epigenetic/H3K9ac tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K4me1 WE - NF29/30 ChIP-Seq NF29/30 embryo Hontelez S et al. (2015) GSM1659900 ChIP-Seq/Epigenetic/H3K4me1 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K27me3 WE - NF8 ChIP-Seq NF8 embryo Hontelez S et al. (2015) GSM1659932 ChIP-Seq/Epigenetic/H3K27me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K9ac WE - NF8 ChIP-Seq NF8 embryo Hontelez S et al. (2015) GSM1659909 ChIP-Seq/Epigenetic/H3K9ac tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 WE - NF9 Bisulfite-Seq NF9 embryo Hontelez S et al. (2015) GSM1875285 Bisulfite-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/Bisulfite-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/Bisulfite-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/Bisulfite-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/Bisulfite-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/Bisulfite-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/Bisulfite-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 ep300 WE - NF9 ChIP-Seq NF9 embryo Hontelez S et al. (2015) GSM1659920 ChIP-Seq/Transcription Factor/ep300 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K9me2 WE - NF9 ChIP-Seq NF9 embryo Hontelez S et al. (2015) GSM1659940 ChIP-Seq/Epigenetic/H3K9me2 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K4me1 WE - NF9 ChIP-Seq NF9 embryo Hontelez S et al. (2015) GSM1659896 ChIP-Seq/Epigenetic/H3K4me1 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 67974 Saartje Hontelez Embryonic transcription is controlled by maternally defined chromatin state During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origi Saartje Hontelez, GertJan Veenstra We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA 26679111 51677 SRP057395 H3K36me3 WE - NF9 ChIP-Seq NF9 embryo Hontelez S et al. (2015) GSM1659915 ChIP-Seq/Epigenetic/H3K36me3 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/Readme.txt 68087 Ozren Bogdanovic Active DNA demethylation at enhancers during the vertebrate phylotypic period The vertebrate body plan and organs are shaped during a conserved embryonic phase called the phylotypic stage, however the mechanisms that guide the e Ozren Bogdanovic, Ryan Lister MethylC-Seq in zebrafish embryos, MethylC-seq in Xenopus tropicalis embryos, MethylC-seq in mouse embryos, MethylC-seq in zebrafish tissues, MethylC-seq in Xenopus tropicalis tissues, TAB-seq in zebrafish embryos, TAB-seq in Xenopus tropicalis embryos, TAB-seq in mouse embryos, RNA-seq in zebrafish embryos, RNA-seq in mouse embryos 26928226 51922 SRP057505 WE - NF29/30 Bisulfite-Seq NF29/30 embryo Bogdanović O et al. (2016) GSM1662791 Bisulfite-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/Readme.txt 68087 Ozren Bogdanovic Active DNA demethylation at enhancers during the vertebrate phylotypic period The vertebrate body plan and organs are shaped during a conserved embryonic phase called the phylotypic stage, however the mechanisms that guide the e Ozren Bogdanovic, Ryan Lister MethylC-Seq in zebrafish embryos, MethylC-seq in Xenopus tropicalis embryos, MethylC-seq in mouse embryos, MethylC-seq in zebrafish tissues, MethylC-seq in Xenopus tropicalis tissues, TAB-seq in zebrafish embryos, TAB-seq in Xenopus tropicalis embryos, TAB-seq in mouse embryos, RNA-seq in zebrafish embryos, RNA-seq in mouse embryos 26928226 51922 SRP057505 WE - NF9 Bisulfite-Seq NF9 embryo Bogdanović O et al. (2016) GSM1662787 Bisulfite-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/Readme.txt 68087 Ozren Bogdanovic Active DNA demethylation at enhancers during the vertebrate phylotypic period The vertebrate body plan and organs are shaped during a conserved embryonic phase called the phylotypic stage, however the mechanisms that guide the e Ozren Bogdanovic, Ryan Lister MethylC-Seq in zebrafish embryos, MethylC-seq in Xenopus tropicalis embryos, MethylC-seq in mouse embryos, MethylC-seq in zebrafish tissues, MethylC-seq in Xenopus tropicalis tissues, TAB-seq in zebrafish embryos, TAB-seq in Xenopus tropicalis embryos, TAB-seq in mouse embryos, RNA-seq in zebrafish embryos, RNA-seq in mouse embryos 26928226 51922 SRP057505 WE - NF12 Bisulfite-Seq NF12 embryo Bogdanović O et al. (2016) GSM1662788 Bisulfite-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/Readme.txt 68087 Ozren Bogdanovic Active DNA demethylation at enhancers during the vertebrate phylotypic period The vertebrate body plan and organs are shaped during a conserved embryonic phase called the phylotypic stage, however the mechanisms that guide the e Ozren Bogdanovic, Ryan Lister MethylC-Seq in zebrafish embryos, MethylC-seq in Xenopus tropicalis embryos, MethylC-seq in mouse embryos, MethylC-seq in zebrafish tissues, MethylC-seq in Xenopus tropicalis tissues, TAB-seq in zebrafish embryos, TAB-seq in Xenopus tropicalis embryos, TAB-seq in mouse embryos, RNA-seq in zebrafish embryos, RNA-seq in mouse embryos 26928226 51922 SRP057505 WE - NF29/30 Bisulfite-Seq NF29/30 embryo Bogdanović O et al. (2016) GSM1662789 Bisulfite-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/Readme.txt 68087 Ozren Bogdanovic Active DNA demethylation at enhancers during the vertebrate phylotypic period The vertebrate body plan and organs are shaped during a conserved embryonic phase called the phylotypic stage, however the mechanisms that guide the e Ozren Bogdanovic, Ryan Lister MethylC-Seq in zebrafish embryos, MethylC-seq in Xenopus tropicalis embryos, MethylC-seq in mouse embryos, MethylC-seq in zebrafish tissues, MethylC-seq in Xenopus tropicalis tissues, TAB-seq in zebrafish embryos, TAB-seq in Xenopus tropicalis embryos, TAB-seq in mouse embryos, RNA-seq in zebrafish embryos, RNA-seq in mouse embryos 26928226 51922 SRP057505 WE - NF43 Bisulfite-Seq NF43 embryo Bogdanović O et al. (2016) GSM1662790 Bisulfite-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/Readme.txt 68087 Ozren Bogdanovic Active DNA demethylation at enhancers during the vertebrate phylotypic period The vertebrate body plan and organs are shaped during a conserved embryonic phase called the phylotypic stage, however the mechanisms that guide the e Ozren Bogdanovic, Ryan Lister MethylC-Seq in zebrafish embryos, MethylC-seq in Xenopus tropicalis embryos, MethylC-seq in mouse embryos, MethylC-seq in zebrafish tissues, MethylC-seq in Xenopus tropicalis tissues, TAB-seq in zebrafish embryos, TAB-seq in Xenopus tropicalis embryos, TAB-seq in mouse embryos, RNA-seq in zebrafish embryos, RNA-seq in mouse embryos 26928226 51922 SRP057505 brain - adult Bisulfite-Seq adult brain Bogdanović O et al. (2016) GSM1859499 Bisulfite-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68087/XENTR_10.0/Bisulfite-Seq/Readme.txt 68972 Xiaopeng Ma The identification of differentially expressed genes between animal and vegetal blastomeres in Xenopus laevis To identify asymmetrically localized maternal mRNAs along the animal-vegetal axis in cleavage Xenopus embryos, we isolated animal and vegetal blastome Xiaopeng Ma, Guanni Sun, Zhirui Hu, Zheying Min, Xiaohua Yan, Zhenpo Guan, Hanxia Su, Yu Fu, YeGuang Chen, Michael Zhang, Qinghua Tao, Wei Wu RNAseq of animal and vegetal blastomeres with 2 biological replicates 26013826 50741 SRP058428 vegetal blastomere - NF4 RNA-Seq NF4 vegetal blastomere Sun G et al. (2015) GSM1689109,GSM1689110 RNA-Seq/Embryonic Tissues/Cleavage NF2- to NF6.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68972 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68972/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68972/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68972/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68972/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68972/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68972/XENLA_10.1/RNA-Seq/Readme.txt 68972 Xiaopeng Ma The identification of differentially expressed genes between animal and vegetal blastomeres in Xenopus laevis To identify asymmetrically localized maternal mRNAs along the animal-vegetal axis in cleavage Xenopus embryos, we isolated animal and vegetal blastome Xiaopeng Ma, Guanni Sun, Zhirui Hu, Zheying Min, Xiaohua Yan, Zhenpo Guan, Hanxia Su, Yu Fu, YeGuang Chen, Michael Zhang, Qinghua Tao, Wei Wu RNAseq of animal and vegetal blastomeres with 2 biological replicates 26013826 50741 SRP058428 animal blastomere - NF4 RNA-Seq NF4 animal blastomere Sun G et al. (2015) GSM1689111,GSM1689112 RNA-Seq/Embryonic Tissues/Cleavage NF2- to NF6.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68972 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68972/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68972/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68972/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68972/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68972/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE68972/XENLA_10.1/RNA-Seq/Readme.txt 69701 Daniel Ramire-Gordillo RNA-Seq and microarray analysis of the Xenopus inner ear transcriptome discloses orthologous OMIM® genes for hereditary disorders of hearing and balance Purpose: To identify orthologous genes in Xenopus that are implicated in deafness and vestibular disorders in humans and to compare RNA-Seq and microa Daniel Ramire-Gordillo, Daniel Ramirez-Gordillo, TuShun Powers, Casilda Trujillo-Provencio, Jennifer van Velkinburgh, Faye Schilkey, Elba Serrano Inner ear RNA from X. laevis larval stages 56-58 was isolated and shipped to the National Center for Genome Resources, for Illumina-Solexa sequencing or to the Massachusetts Institute of Technology BioMicro Center for microarray analysis with the Affymetrix GeneChip® X. laevis Genome 2.0 Array. RNA-Sequencing was completed using the Illumina-Solexa platform for sequencing by synthesis. Short-insert paired end (SIPE) libraries were prepared from total RNA according to Illumina’s mRNA-Seq Sample Prep Protocol v2.0 (Illumina, San Diego, CA, USA). The resultant double-stranded cDNA concentration was measured on a NanoDrop spectrophotometer, and size and purity were determined on the 2100 Bioanalyzer using a DNA 1000 Nano kit. The cDNA libraries were cluster amplified on Illumina flowcells, sequenced on the GAII Sequencer as 36-cycle single-end reads, and processed using Illumina software v1.0. Illumina reads were aligned to the X. tropicalis genome using the algorithm for genomic mapping and alignment program (GMAP) and Alpheus® Sequence Variant Detection System v3.1. 26582541 51592 SRP059283 inner ear - NF56-58 RNA-Seq NF56 inner ear Ramírez-Gordillo D et al. (2015) GSM1707665 RNA-Seq/Embryonic Tissues/NF56 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE69701 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE69701/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE69701/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE69701/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE69701/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE69701/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE69701/XENLA_10.1/RNA-Seq/Readme.txt 71006 Ferdinand Marlétaz Cdx ParaHox genes acquired distinct developmental roles after gene duplication in vertebrate evolution We examined the degree of regulatory and functional overlap between the three vertebrate Cdx genes using single and triple morpholino knock-down in Xe Ferdinand Marlétaz, Harv Isaacs, Peter Holland Stage 14 (early neurula) embryos derived from eggs injected with morpholinos against Cdx1, Cdx2, Cdx4 and a mixture of all three plus corresponding uninjected embryos. All in triplicates. 26231746 51076 SRP061238 WE + cdx1 MO - NF14 RNA-Seq NF14 embryo Marlétaz F et al. (2015) GSM1825040,GSM1825041,GSM1825042 Manipulations/Morpholino tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/Readme.txt 71006 Ferdinand Marlétaz Cdx ParaHox genes acquired distinct developmental roles after gene duplication in vertebrate evolution We examined the degree of regulatory and functional overlap between the three vertebrate Cdx genes using single and triple morpholino knock-down in Xe Ferdinand Marlétaz, Harv Isaacs, Peter Holland Stage 14 (early neurula) embryos derived from eggs injected with morpholinos against Cdx1, Cdx2, Cdx4 and a mixture of all three plus corresponding uninjected embryos. All in triplicates. 26231746 51076 SRP061238 WE + cdx1 MO - NF14 RNA-Seq NF14 embryo Marlétaz F et al. (2015) GSM1825040,GSM1825041,GSM1825042 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/Readme.txt 71006 Ferdinand Marlétaz Cdx ParaHox genes acquired distinct developmental roles after gene duplication in vertebrate evolution We examined the degree of regulatory and functional overlap between the three vertebrate Cdx genes using single and triple morpholino knock-down in Xe Ferdinand Marlétaz, Harv Isaacs, Peter Holland Stage 14 (early neurula) embryos derived from eggs injected with morpholinos against Cdx1, Cdx2, Cdx4 and a mixture of all three plus corresponding uninjected embryos. All in triplicates. 26231746 51076 SRP061238 WE + Cdx2 MO - NF14 RNA-Seq NF14 embryo Marlétaz F et al. (2015) GSM1825043,GSM1825044,GSM1825045 Manipulations/Morpholino tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/Readme.txt 71006 Ferdinand Marlétaz Cdx ParaHox genes acquired distinct developmental roles after gene duplication in vertebrate evolution We examined the degree of regulatory and functional overlap between the three vertebrate Cdx genes using single and triple morpholino knock-down in Xe Ferdinand Marlétaz, Harv Isaacs, Peter Holland Stage 14 (early neurula) embryos derived from eggs injected with morpholinos against Cdx1, Cdx2, Cdx4 and a mixture of all three plus corresponding uninjected embryos. All in triplicates. 26231746 51076 SRP061238 WE + Cdx2 MO - NF14 RNA-Seq NF14 embryo Marlétaz F et al. (2015) GSM1825043,GSM1825044,GSM1825045 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/Readme.txt 71006 Ferdinand Marlétaz Cdx ParaHox genes acquired distinct developmental roles after gene duplication in vertebrate evolution We examined the degree of regulatory and functional overlap between the three vertebrate Cdx genes using single and triple morpholino knock-down in Xe Ferdinand Marlétaz, Harv Isaacs, Peter Holland Stage 14 (early neurula) embryos derived from eggs injected with morpholinos against Cdx1, Cdx2, Cdx4 and a mixture of all three plus corresponding uninjected embryos. All in triplicates. 26231746 51076 SRP061238 WE + hbg1 MO - NF14 RNA-Seq NF14 embryo Marlétaz F et al. (2015) GSM1825052,GSM1825053,GSM1825054 Manipulations/Morpholino tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/Readme.txt 71006 Ferdinand Marlétaz Cdx ParaHox genes acquired distinct developmental roles after gene duplication in vertebrate evolution We examined the degree of regulatory and functional overlap between the three vertebrate Cdx genes using single and triple morpholino knock-down in Xe Ferdinand Marlétaz, Harv Isaacs, Peter Holland Stage 14 (early neurula) embryos derived from eggs injected with morpholinos against Cdx1, Cdx2, Cdx4 and a mixture of all three plus corresponding uninjected embryos. All in triplicates. 26231746 51076 SRP061238 WE + hbg1 MO - NF14 RNA-Seq NF14 embryo Marlétaz F et al. (2015) GSM1825052,GSM1825053,GSM1825054 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/Readme.txt 71006 Ferdinand Marlétaz Cdx ParaHox genes acquired distinct developmental roles after gene duplication in vertebrate evolution We examined the degree of regulatory and functional overlap between the three vertebrate Cdx genes using single and triple morpholino knock-down in Xe Ferdinand Marlétaz, Harv Isaacs, Peter Holland Stage 14 (early neurula) embryos derived from eggs injected with morpholinos against Cdx1, Cdx2, Cdx4 and a mixture of all three plus corresponding uninjected embryos. All in triplicates. 26231746 51076 SRP061238 WE - NF14 RNA-Seq NF14 embryo Marlétaz F et al. (2015) GSM1825055,GSM1825056,GSM1825057 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/Readme.txt 71006 Ferdinand Marlétaz Cdx ParaHox genes acquired distinct developmental roles after gene duplication in vertebrate evolution We examined the degree of regulatory and functional overlap between the three vertebrate Cdx genes using single and triple morpholino knock-down in Xe Ferdinand Marlétaz, Harv Isaacs, Peter Holland Stage 14 (early neurula) embryos derived from eggs injected with morpholinos against Cdx1, Cdx2, Cdx4 and a mixture of all three plus corresponding uninjected embryos. All in triplicates. 26231746 51076 SRP061238 WE + Cdx4 MO - NF14 RNA-Seq NF14 embryo Marlétaz F et al. (2015) GSM1825046,GSM1825047,GSM1825048 Manipulations/Morpholino tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/Readme.txt 71006 Ferdinand Marlétaz Cdx ParaHox genes acquired distinct developmental roles after gene duplication in vertebrate evolution We examined the degree of regulatory and functional overlap between the three vertebrate Cdx genes using single and triple morpholino knock-down in Xe Ferdinand Marlétaz, Harv Isaacs, Peter Holland Stage 14 (early neurula) embryos derived from eggs injected with morpholinos against Cdx1, Cdx2, Cdx4 and a mixture of all three plus corresponding uninjected embryos. All in triplicates. 26231746 51076 SRP061238 WE + Cdx4 MO - NF14 RNA-Seq NF14 embryo Marlétaz F et al. (2015) GSM1825046,GSM1825047,GSM1825048 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/Readme.txt 71006 Ferdinand Marlétaz Cdx ParaHox genes acquired distinct developmental roles after gene duplication in vertebrate evolution We examined the degree of regulatory and functional overlap between the three vertebrate Cdx genes using single and triple morpholino knock-down in Xe Ferdinand Marlétaz, Harv Isaacs, Peter Holland Stage 14 (early neurula) embryos derived from eggs injected with morpholinos against Cdx1, Cdx2, Cdx4 and a mixture of all three plus corresponding uninjected embryos. All in triplicates. 26231746 51076 SRP061238 WE + cdx1 MO + Cdx2 MO + Cdx4 MO - NF14 RNA-Seq NF14 embryo Marlétaz F et al. (2015) GSM1825049,GSM1825050,GSM1825051 Manipulations/Morpholino tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/Readme.txt 71006 Ferdinand Marlétaz Cdx ParaHox genes acquired distinct developmental roles after gene duplication in vertebrate evolution We examined the degree of regulatory and functional overlap between the three vertebrate Cdx genes using single and triple morpholino knock-down in Xe Ferdinand Marlétaz, Harv Isaacs, Peter Holland Stage 14 (early neurula) embryos derived from eggs injected with morpholinos against Cdx1, Cdx2, Cdx4 and a mixture of all three plus corresponding uninjected embryos. All in triplicates. 26231746 51076 SRP061238 WE + cdx1 MO + Cdx2 MO + Cdx4 MO - NF14 RNA-Seq NF14 embryo Marlétaz F et al. (2015) GSM1825049,GSM1825050,GSM1825051 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE71006/XENTR_10.0/RNA-Seq/Readme.txt 72657 Stefan Hoppler Tissue- and stage-specific cellular context regulates Wnt target gene expression subsequent to β-catenin recruitment The aim of our study is to identify direct target genes of Wnt/β-catenin signaling operating in gastrula-stage X. tropicalis embryos. We characterized Stefan Hoppler, Yukio Nakamura, Eduardo Alves For ChIP-seq, one ChIP DNA and one input control DNA samples pooled from three independent ChIP experiments using early gastrula embryos were sequenced. For RNA-seq, Twelve total RNA samples (triplicates of each experimental samples: uninjected, CoMO-injected, wnt8aMO-injected, wnt8aMO and pCSKA-wnt8a-coinjected) from early gastrula embryos were sequenced. 27068107 52077 SRP063109 WE + wnt8a MO + wnt8a - NF10.25 RNA-Seq NF10.25 embryo Nakamura Y et al. (2016) GSM1867405,GSM1867409,GSM1867413 Manipulations/Morpholino tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/Readme.txt 72657 Stefan Hoppler Tissue- and stage-specific cellular context regulates Wnt target gene expression subsequent to β-catenin recruitment The aim of our study is to identify direct target genes of Wnt/β-catenin signaling operating in gastrula-stage X. tropicalis embryos. We characterized Stefan Hoppler, Yukio Nakamura, Eduardo Alves For ChIP-seq, one ChIP DNA and one input control DNA samples pooled from three independent ChIP experiments using early gastrula embryos were sequenced. For RNA-seq, Twelve total RNA samples (triplicates of each experimental samples: uninjected, CoMO-injected, wnt8aMO-injected, wnt8aMO and pCSKA-wnt8a-coinjected) from early gastrula embryos were sequenced. 27068107 52077 SRP063109 WE + wnt8a MO + wnt8a - NF10.25 RNA-Seq NF10.25 embryo Nakamura Y et al. (2016) GSM1867405,GSM1867409,GSM1867413 Manipulations/mRNA Injection tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/Readme.txt 72657 Stefan Hoppler Tissue- and stage-specific cellular context regulates Wnt target gene expression subsequent to β-catenin recruitment The aim of our study is to identify direct target genes of Wnt/β-catenin signaling operating in gastrula-stage X. tropicalis embryos. We characterized Stefan Hoppler, Yukio Nakamura, Eduardo Alves For ChIP-seq, one ChIP DNA and one input control DNA samples pooled from three independent ChIP experiments using early gastrula embryos were sequenced. For RNA-seq, Twelve total RNA samples (triplicates of each experimental samples: uninjected, CoMO-injected, wnt8aMO-injected, wnt8aMO and pCSKA-wnt8a-coinjected) from early gastrula embryos were sequenced. 27068107 52077 SRP063109 WE + wnt8a MO + wnt8a - NF10.25 RNA-Seq NF10.25 embryo Nakamura Y et al. (2016) GSM1867405,GSM1867409,GSM1867413 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/Readme.txt 72657 Stefan Hoppler Tissue- and stage-specific cellular context regulates Wnt target gene expression subsequent to β-catenin recruitment The aim of our study is to identify direct target genes of Wnt/β-catenin signaling operating in gastrula-stage X. tropicalis embryos. We characterized Stefan Hoppler, Yukio Nakamura, Eduardo Alves For ChIP-seq, one ChIP DNA and one input control DNA samples pooled from three independent ChIP experiments using early gastrula embryos were sequenced. For RNA-seq, Twelve total RNA samples (triplicates of each experimental samples: uninjected, CoMO-injected, wnt8aMO-injected, wnt8aMO and pCSKA-wnt8a-coinjected) from early gastrula embryos were sequenced. 27068107 52077 SRP063109 input WE - NF10.25 ChIP-Seq NF10.25 embryo Nakamura Y et al. (2016) GSM1867401 None tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/ChIP-Seq/Readme.txt 72657 Stefan Hoppler Tissue- and stage-specific cellular context regulates Wnt target gene expression subsequent to β-catenin recruitment The aim of our study is to identify direct target genes of Wnt/β-catenin signaling operating in gastrula-stage X. tropicalis embryos. We characterized Stefan Hoppler, Yukio Nakamura, Eduardo Alves For ChIP-seq, one ChIP DNA and one input control DNA samples pooled from three independent ChIP experiments using early gastrula embryos were sequenced. For RNA-seq, Twelve total RNA samples (triplicates of each experimental samples: uninjected, CoMO-injected, wnt8aMO-injected, wnt8aMO and pCSKA-wnt8a-coinjected) from early gastrula embryos were sequenced. 27068107 52077 SRP063109 WE - NF10.25 RNA-Seq NF10.25 embryo Nakamura Y et al. (2016) GSM1867402,GSM1867406,GSM1867410 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/Readme.txt 72657 Stefan Hoppler Tissue- and stage-specific cellular context regulates Wnt target gene expression subsequent to β-catenin recruitment The aim of our study is to identify direct target genes of Wnt/β-catenin signaling operating in gastrula-stage X. tropicalis embryos. We characterized Stefan Hoppler, Yukio Nakamura, Eduardo Alves For ChIP-seq, one ChIP DNA and one input control DNA samples pooled from three independent ChIP experiments using early gastrula embryos were sequenced. For RNA-seq, Twelve total RNA samples (triplicates of each experimental samples: uninjected, CoMO-injected, wnt8aMO-injected, wnt8aMO and pCSKA-wnt8a-coinjected) from early gastrula embryos were sequenced. 27068107 52077 SRP063109 WE + hbg1 MO - NF10.25 RNA-Seq NF10.25 embryo Nakamura Y et al. (2016) GSM1867403,GSM1867407,GSM1867411 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/Readme.txt 72657 Stefan Hoppler Tissue- and stage-specific cellular context regulates Wnt target gene expression subsequent to β-catenin recruitment The aim of our study is to identify direct target genes of Wnt/β-catenin signaling operating in gastrula-stage X. tropicalis embryos. We characterized Stefan Hoppler, Yukio Nakamura, Eduardo Alves For ChIP-seq, one ChIP DNA and one input control DNA samples pooled from three independent ChIP experiments using early gastrula embryos were sequenced. For RNA-seq, Twelve total RNA samples (triplicates of each experimental samples: uninjected, CoMO-injected, wnt8aMO-injected, wnt8aMO and pCSKA-wnt8a-coinjected) from early gastrula embryos were sequenced. 27068107 52077 SRP063109 WE + hbg1 MO - NF10.25 RNA-Seq NF10.25 embryo Nakamura Y et al. (2016) GSM1867403,GSM1867407,GSM1867411 Manipulations/Morpholino tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/Readme.txt 72657 Stefan Hoppler Tissue- and stage-specific cellular context regulates Wnt target gene expression subsequent to β-catenin recruitment The aim of our study is to identify direct target genes of Wnt/β-catenin signaling operating in gastrula-stage X. tropicalis embryos. We characterized Stefan Hoppler, Yukio Nakamura, Eduardo Alves For ChIP-seq, one ChIP DNA and one input control DNA samples pooled from three independent ChIP experiments using early gastrula embryos were sequenced. For RNA-seq, Twelve total RNA samples (triplicates of each experimental samples: uninjected, CoMO-injected, wnt8aMO-injected, wnt8aMO and pCSKA-wnt8a-coinjected) from early gastrula embryos were sequenced. 27068107 52077 SRP063109 WE + wnt8a MO - NF10.25 RNA-Seq NF10.25 embryo Nakamura Y et al. (2016) GSM1867404,GSM1867408,GSM1867412 Manipulations/Morpholino tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/Readme.txt 72657 Stefan Hoppler Tissue- and stage-specific cellular context regulates Wnt target gene expression subsequent to β-catenin recruitment The aim of our study is to identify direct target genes of Wnt/β-catenin signaling operating in gastrula-stage X. tropicalis embryos. We characterized Stefan Hoppler, Yukio Nakamura, Eduardo Alves For ChIP-seq, one ChIP DNA and one input control DNA samples pooled from three independent ChIP experiments using early gastrula embryos were sequenced. For RNA-seq, Twelve total RNA samples (triplicates of each experimental samples: uninjected, CoMO-injected, wnt8aMO-injected, wnt8aMO and pCSKA-wnt8a-coinjected) from early gastrula embryos were sequenced. 27068107 52077 SRP063109 WE + wnt8a MO - NF10.25 RNA-Seq NF10.25 embryo Nakamura Y et al. (2016) GSM1867404,GSM1867408,GSM1867412 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/Readme.txt 72657 Stefan Hoppler Tissue- and stage-specific cellular context regulates Wnt target gene expression subsequent to β-catenin recruitment The aim of our study is to identify direct target genes of Wnt/β-catenin signaling operating in gastrula-stage X. tropicalis embryos. We characterized Stefan Hoppler, Yukio Nakamura, Eduardo Alves For ChIP-seq, one ChIP DNA and one input control DNA samples pooled from three independent ChIP experiments using early gastrula embryos were sequenced. For RNA-seq, Twelve total RNA samples (triplicates of each experimental samples: uninjected, CoMO-injected, wnt8aMO-injected, wnt8aMO and pCSKA-wnt8a-coinjected) from early gastrula embryos were sequenced. 27068107 52077 SRP063109 beta Catenin WE - NF10.25 ChIP-Seq NF10.25 embryo Nakamura Y et al. (2016) GSM1867400 ChIP-Seq/Transcription Factor/beta Catenin tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE72657/XENTR_10.0/ChIP-Seq/Readme.txt 73419 Taejoon Kwon Tissue gene expression of Xenopus laevis J strain [tissue] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different tissues, as a part of the Xenopus laevis genome project. Th Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole tissue; two female frogs were used as donors for most tissues (Taira dataset for one frog, Ueno dataset for the other frog); testis samples were collected from two male frogs (sibling of two female donors) 27762356 52612 SRP064167 pancreas - adult RNA-Seq adult pancreas Session AM et al. (2016) GSM1893248,GSM1893262 RNA-Seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Readme.txt 73419 Taejoon Kwon Tissue gene expression of Xenopus laevis J strain [tissue] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different tissues, as a part of the Xenopus laevis genome project. Th Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole tissue; two female frogs were used as donors for most tissues (Taira dataset for one frog, Ueno dataset for the other frog); testis samples were collected from two male frogs (sibling of two female donors) 27762356 52612 SRP064167 heart - adult RNA-Seq adult heart Session AM et al. (2016) GSM1893241,GSM1893255 RNA-Seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Readme.txt 73419 Taejoon Kwon Tissue gene expression of Xenopus laevis J strain [tissue] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different tissues, as a part of the Xenopus laevis genome project. Th Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole tissue; two female frogs were used as donors for most tissues (Taira dataset for one frog, Ueno dataset for the other frog); testis samples were collected from two male frogs (sibling of two female donors) 27762356 52612 SRP064167 testis - adult RNA-Seq adult testis Session AM et al. (2016) GSM1893252,GSM1893266 RNA-Seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Readme.txt 73419 Taejoon Kwon Tissue gene expression of Xenopus laevis J strain [tissue] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different tissues, as a part of the Xenopus laevis genome project. Th Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole tissue; two female frogs were used as donors for most tissues (Taira dataset for one frog, Ueno dataset for the other frog); testis samples were collected from two male frogs (sibling of two female donors) 27762356 52612 SRP064167 brain - adult RNA-Seq adult brain Session AM et al. (2016) GSM1893239,GSM1893253 RNA-Seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Readme.txt 73419 Taejoon Kwon Tissue gene expression of Xenopus laevis J strain [tissue] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different tissues, as a part of the Xenopus laevis genome project. Th Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole tissue; two female frogs were used as donors for most tissues (Taira dataset for one frog, Ueno dataset for the other frog); testis samples were collected from two male frogs (sibling of two female donors) 27762356 52612 SRP064167 liver - adult RNA-Seq adult liver Session AM et al. (2016) GSM1893244,GSM1893258 RNA-Seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Readme.txt 73419 Taejoon Kwon Tissue gene expression of Xenopus laevis J strain [tissue] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different tissues, as a part of the Xenopus laevis genome project. Th Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole tissue; two female frogs were used as donors for most tissues (Taira dataset for one frog, Ueno dataset for the other frog); testis samples were collected from two male frogs (sibling of two female donors) 27762356 52612 SRP064167 kidney - adult RNA-Seq adult kidney Session AM et al. (2016) GSM1893243,GSM1893257 RNA-Seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Readme.txt 73419 Taejoon Kwon Tissue gene expression of Xenopus laevis J strain [tissue] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different tissues, as a part of the Xenopus laevis genome project. Th Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole tissue; two female frogs were used as donors for most tissues (Taira dataset for one frog, Ueno dataset for the other frog); testis samples were collected from two male frogs (sibling of two female donors) 27762356 52612 SRP064167 ovary - adult RNA-Seq adult ovary Session AM et al. (2016) GSM1893247,GSM1893261 RNA-Seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Readme.txt 73419 Taejoon Kwon Tissue gene expression of Xenopus laevis J strain [tissue] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different tissues, as a part of the Xenopus laevis genome project. Th Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole tissue; two female frogs were used as donors for most tissues (Taira dataset for one frog, Ueno dataset for the other frog); testis samples were collected from two male frogs (sibling of two female donors) 27762356 52612 SRP064167 stomach - adult RNA-Seq adult stomach Session AM et al. (2016) GSM1893251,GSM1893265 RNA-Seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Readme.txt 73419 Taejoon Kwon Tissue gene expression of Xenopus laevis J strain [tissue] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different tissues, as a part of the Xenopus laevis genome project. Th Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole tissue; two female frogs were used as donors for most tissues (Taira dataset for one frog, Ueno dataset for the other frog); testis samples were collected from two male frogs (sibling of two female donors) 27762356 52612 SRP064167 eye - adult RNA-Seq adult eye Session AM et al. (2016) GSM1893240,GSM1893254 RNA-Seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Readme.txt 73419 Taejoon Kwon Tissue gene expression of Xenopus laevis J strain [tissue] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different tissues, as a part of the Xenopus laevis genome project. Th Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole tissue; two female frogs were used as donors for most tissues (Taira dataset for one frog, Ueno dataset for the other frog); testis samples were collected from two male frogs (sibling of two female donors) 27762356 52612 SRP064167 intestine - adult RNA-Seq adult intestine Session AM et al. (2016) GSM1893242,GSM1893256 RNA-Seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Readme.txt 73419 Taejoon Kwon Tissue gene expression of Xenopus laevis J strain [tissue] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different tissues, as a part of the Xenopus laevis genome project. Th Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole tissue; two female frogs were used as donors for most tissues (Taira dataset for one frog, Ueno dataset for the other frog); testis samples were collected from two male frogs (sibling of two female donors) 27762356 52612 SRP064167 lung - adult RNA-Seq adult lung Session AM et al. (2016) GSM1893245,GSM1893259 RNA-Seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Readme.txt 73419 Taejoon Kwon Tissue gene expression of Xenopus laevis J strain [tissue] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different tissues, as a part of the Xenopus laevis genome project. Th Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole tissue; two female frogs were used as donors for most tissues (Taira dataset for one frog, Ueno dataset for the other frog); testis samples were collected from two male frogs (sibling of two female donors) 27762356 52612 SRP064167 muscle - adult RNA-Seq adult muscle Session AM et al. (2016) GSM1893246,GSM1893260 RNA-Seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Readme.txt 73419 Taejoon Kwon Tissue gene expression of Xenopus laevis J strain [tissue] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different tissues, as a part of the Xenopus laevis genome project. Th Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole tissue; two female frogs were used as donors for most tissues (Taira dataset for one frog, Ueno dataset for the other frog); testis samples were collected from two male frogs (sibling of two female donors) 27762356 52612 SRP064167 skin - adult RNA-Seq adult skin Session AM et al. (2016) GSM1893249,GSM1893263 RNA-Seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Readme.txt 73419 Taejoon Kwon Tissue gene expression of Xenopus laevis J strain [tissue] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different tissues, as a part of the Xenopus laevis genome project. Th Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole tissue; two female frogs were used as donors for most tissues (Taira dataset for one frog, Ueno dataset for the other frog); testis samples were collected from two male frogs (sibling of two female donors) 27762356 52612 SRP064167 spleen - adult RNA-Seq adult spleen Session AM et al. (2016) GSM1893250,GSM1893264 RNA-Seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73419/XENLA_10.1/RNA-Seq/Readme.txt 73430 Taejoon Kwon Developmental gene expression of Xenopus laevis J strain [stage] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different developmental stages, as a part of the Xenopus laevis genom Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole embryos; two clutches were used (Taira dataset for one pair, Ueno dataset for the other pair) 27762356 52612 SRP064186 WE - NF9 RNA-Seq NF9 embryo Session AM et al. (2016) GSM1893585,GSM1893599 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Readme.txt 73430 Taejoon Kwon Developmental gene expression of Xenopus laevis J strain [stage] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different developmental stages, as a part of the Xenopus laevis genom Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole embryos; two clutches were used (Taira dataset for one pair, Ueno dataset for the other pair) 27762356 52612 SRP064186 WE - NF35/36 RNA-Seq NF35/36 embryo Session AM et al. (2016) GSM1893592,GSM1893606,GSM1893610 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Readme.txt 73430 Taejoon Kwon Developmental gene expression of Xenopus laevis J strain [stage] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different developmental stages, as a part of the Xenopus laevis genom Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole embryos; two clutches were used (Taira dataset for one pair, Ueno dataset for the other pair) 27762356 52612 SRP064186 oocyte - oocyte V-VI RNA-Seq oocyte V oocyte Session AM et al. (2016) GSM1893597 RNA-Seq/Embryonic Tissues/unfertilized egg laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Readme.txt 73430 Taejoon Kwon Developmental gene expression of Xenopus laevis J strain [stage] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different developmental stages, as a part of the Xenopus laevis genom Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole embryos; two clutches were used (Taira dataset for one pair, Ueno dataset for the other pair) 27762356 52612 SRP064186 WE - NF12 RNA-Seq NF12 embryo Session AM et al. (2016) GSM1893587,GSM1893601 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Readme.txt 73430 Taejoon Kwon Developmental gene expression of Xenopus laevis J strain [stage] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different developmental stages, as a part of the Xenopus laevis genom Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole embryos; two clutches were used (Taira dataset for one pair, Ueno dataset for the other pair) 27762356 52612 SRP064186 WE - NF15 RNA-Seq NF15 embryo Session AM et al. (2016) GSM1893588,GSM1893602 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Readme.txt 73430 Taejoon Kwon Developmental gene expression of Xenopus laevis J strain [stage] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different developmental stages, as a part of the Xenopus laevis genom Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole embryos; two clutches were used (Taira dataset for one pair, Ueno dataset for the other pair) 27762356 52612 SRP064186 WE - NF8 RNA-Seq NF8 embryo Session AM et al. (2016) GSM1893584,GSM1893598,GSM1893608 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Readme.txt 73430 Taejoon Kwon Developmental gene expression of Xenopus laevis J strain [stage] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different developmental stages, as a part of the Xenopus laevis genom Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole embryos; two clutches were used (Taira dataset for one pair, Ueno dataset for the other pair) 27762356 52612 SRP064186 oocyte - oocyte I-II RNA-Seq oocyte I oocyte Session AM et al. (2016) GSM1893595 RNA-Seq/Embryonic Tissues/unfertilized egg laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Readme.txt 73430 Taejoon Kwon Developmental gene expression of Xenopus laevis J strain [stage] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different developmental stages, as a part of the Xenopus laevis genom Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole embryos; two clutches were used (Taira dataset for one pair, Ueno dataset for the other pair) 27762356 52612 SRP064186 oocyte - oocyte III-IV RNA-Seq oocyte III oocyte Session AM et al. (2016) GSM1893596 RNA-Seq/Embryonic Tissues/unfertilized egg laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Readme.txt 73430 Taejoon Kwon Developmental gene expression of Xenopus laevis J strain [stage] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different developmental stages, as a part of the Xenopus laevis genom Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole embryos; two clutches were used (Taira dataset for one pair, Ueno dataset for the other pair) 27762356 52612 SRP064186 WE - NF10-10.5 RNA-Seq NF10 embryo Session AM et al. (2016) GSM1893586,GSM1893600,GSM1893609 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Readme.txt 73430 Taejoon Kwon Developmental gene expression of Xenopus laevis J strain [stage] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different developmental stages, as a part of the Xenopus laevis genom Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole embryos; two clutches were used (Taira dataset for one pair, Ueno dataset for the other pair) 27762356 52612 SRP064186 WE - NF20 RNA-Seq NF20 embryo Session AM et al. (2016) GSM1893589,GSM1893603 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Readme.txt 73430 Taejoon Kwon Developmental gene expression of Xenopus laevis J strain [stage] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different developmental stages, as a part of the Xenopus laevis genom Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole embryos; two clutches were used (Taira dataset for one pair, Ueno dataset for the other pair) 27762356 52612 SRP064186 WE - NF25 RNA-Seq NF25 embryo Session AM et al. (2016) GSM1893590,GSM1893604 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Readme.txt 73430 Taejoon Kwon Developmental gene expression of Xenopus laevis J strain [stage] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different developmental stages, as a part of the Xenopus laevis genom Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole embryos; two clutches were used (Taira dataset for one pair, Ueno dataset for the other pair) 27762356 52612 SRP064186 WE - NF29/30 RNA-Seq NF29/30 embryo Session AM et al. (2016) GSM1893591,GSM1893605 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Readme.txt 73430 Taejoon Kwon Developmental gene expression of Xenopus laevis J strain [stage] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different developmental stages, as a part of the Xenopus laevis genom Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole embryos; two clutches were used (Taira dataset for one pair, Ueno dataset for the other pair) 27762356 52612 SRP064186 WE - NF40 RNA-Seq NF40 embryo Session AM et al. (2016) GSM1893593,GSM1893607 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Readme.txt 73430 Taejoon Kwon Developmental gene expression of Xenopus laevis J strain [stage] Comprehensive RNA-seq experiments to measure the expression of homoeologs across different developmental stages, as a part of the Xenopus laevis genom Taejoon Kwon, Shuji Takahashi, Yutaka Suzuki, Atsushi Toyoda, Naoto Ueno, Masanori Taira Collect mRNA from whole embryos; two clutches were used (Taira dataset for one pair, Ueno dataset for the other pair) 27762356 52612 SRP064186 egg - unfertilized egg RNA-Seq egg egg Session AM et al. (2016) GSM1893583,GSM1893594 RNA-Seq/Embryonic Tissues/unfertilized egg laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73430/XENLA_10.1/RNA-Seq/Readme.txt 73870 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [polyA] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by Poly(A) extraction using Dynabeads (invitrogen) and the EpiCenter ScripSeq kit V1 using 50-300ng input RNA, and 10 cycles amplification. 26555057 51556 SRP064629 WE - NF29/30 RNA-Seq NF29/30 embryo Peshkin L et al. (2015) GSM1904679 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Readme.txt 73870 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [polyA] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by Poly(A) extraction using Dynabeads (invitrogen) and the EpiCenter ScripSeq kit V1 using 50-300ng input RNA, and 10 cycles amplification. 26555057 51556 SRP064629 WE - NF14 RNA-Seq NF14 embryo Peshkin L et al. (2015) GSM1904673 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Readme.txt 73870 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [polyA] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by Poly(A) extraction using Dynabeads (invitrogen) and the EpiCenter ScripSeq kit V1 using 50-300ng input RNA, and 10 cycles amplification. 26555057 51556 SRP064629 WE - mature egg RNA-Seq mature egg embryo Peshkin L et al. (2015) GSM1904663 RNA-Seq/Whole Embryo/unfertilized egg laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Readme.txt 73870 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [polyA] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by Poly(A) extraction using Dynabeads (invitrogen) and the EpiCenter ScripSeq kit V1 using 50-300ng input RNA, and 10 cycles amplification. 26555057 51556 SRP064629 WE - NF18 RNA-Seq NF18 embryo Peshkin L et al. (2015) GSM1904675 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Readme.txt 73870 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [polyA] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by Poly(A) extraction using Dynabeads (invitrogen) and the EpiCenter ScripSeq kit V1 using 50-300ng input RNA, and 10 cycles amplification. 26555057 51556 SRP064629 WE - NF12 RNA-Seq NF12 embryo Peshkin L et al. (2015) GSM1904672 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Readme.txt 73870 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [polyA] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by Poly(A) extraction using Dynabeads (invitrogen) and the EpiCenter ScripSeq kit V1 using 50-300ng input RNA, and 10 cycles amplification. 26555057 51556 SRP064629 WE - NF2 RNA-Seq NF2 embryo Peshkin L et al. (2015) GSM1904664 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Readme.txt 73870 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [polyA] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by Poly(A) extraction using Dynabeads (invitrogen) and the EpiCenter ScripSeq kit V1 using 50-300ng input RNA, and 10 cycles amplification. 26555057 51556 SRP064629 WE - NF26 RNA-Seq NF26 embryo Peshkin L et al. (2015) GSM1904678 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Readme.txt 73870 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [polyA] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by Poly(A) extraction using Dynabeads (invitrogen) and the EpiCenter ScripSeq kit V1 using 50-300ng input RNA, and 10 cycles amplification. 26555057 51556 SRP064629 WE - NF7 RNA-Seq NF7 embryo Peshkin L et al. (2015) GSM1904667 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Readme.txt 73870 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [polyA] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by Poly(A) extraction using Dynabeads (invitrogen) and the EpiCenter ScripSeq kit V1 using 50-300ng input RNA, and 10 cycles amplification. 26555057 51556 SRP064629 WE - NF9 RNA-Seq NF9 embryo Peshkin L et al. (2015) GSM1904670 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Readme.txt 73870 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [polyA] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by Poly(A) extraction using Dynabeads (invitrogen) and the EpiCenter ScripSeq kit V1 using 50-300ng input RNA, and 10 cycles amplification. 26555057 51556 SRP064629 WE - NF33/34 RNA-Seq NF33/34 embryo Peshkin L et al. (2015) GSM1904680 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Readme.txt 73870 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [polyA] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by Poly(A) extraction using Dynabeads (invitrogen) and the EpiCenter ScripSeq kit V1 using 50-300ng input RNA, and 10 cycles amplification. 26555057 51556 SRP064629 WE - NF6 RNA-Seq NF6 embryo Peshkin L et al. (2015) GSM1904665 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Readme.txt 73870 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [polyA] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by Poly(A) extraction using Dynabeads (invitrogen) and the EpiCenter ScripSeq kit V1 using 50-300ng input RNA, and 10 cycles amplification. 26555057 51556 SRP064629 WE - NF20 RNA-Seq NF20 embryo Peshkin L et al. (2015) GSM1904676 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Readme.txt 73870 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [polyA] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by Poly(A) extraction using Dynabeads (invitrogen) and the EpiCenter ScripSeq kit V1 using 50-300ng input RNA, and 10 cycles amplification. 26555057 51556 SRP064629 WE - NF8 RNA-Seq NF8 embryo Peshkin L et al. (2015) GSM1904668,GSM1904669 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Readme.txt 73870 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [polyA] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by Poly(A) extraction using Dynabeads (invitrogen) and the EpiCenter ScripSeq kit V1 using 50-300ng input RNA, and 10 cycles amplification. 26555057 51556 SRP064629 WE - NF10 RNA-Seq NF10 embryo Peshkin L et al. (2015) GSM1904671 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Readme.txt 73870 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [polyA] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by Poly(A) extraction using Dynabeads (invitrogen) and the EpiCenter ScripSeq kit V1 using 50-300ng input RNA, and 10 cycles amplification. 26555057 51556 SRP064629 WE - NF16 RNA-Seq NF16 embryo Peshkin L et al. (2015) GSM1904674 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Readme.txt 73870 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [polyA] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by Poly(A) extraction using Dynabeads (invitrogen) and the EpiCenter ScripSeq kit V1 using 50-300ng input RNA, and 10 cycles amplification. 26555057 51556 SRP064629 WE - NF23 RNA-Seq NF23 embryo Peshkin L et al. (2015) GSM1904677 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Readme.txt 73870 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [polyA] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by Poly(A) extraction using Dynabeads (invitrogen) and the EpiCenter ScripSeq kit V1 using 50-300ng input RNA, and 10 cycles amplification. 26555057 51556 SRP064629 WE - NF6.5 RNA-Seq NF6.5 embryo Peshkin L et al. (2015) GSM1904666 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73870/XENLA_10.1/RNA-Seq/Readme.txt 73904 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [RiboZero] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 12 cycles amplification. 26555057 51556 SRP064686 WE - NF20 RNA-Seq NF20 embryo Peshkin L et al. (2015) GSM1905650 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Readme.txt 73904 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [RiboZero] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 12 cycles amplification. 26555057 51556 SRP064686 WE - NF33/34 RNA-Seq NF33/34 embryo Peshkin L et al. (2015) GSM1905654 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Readme.txt 73904 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [RiboZero] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 12 cycles amplification. 26555057 51556 SRP064686 WE - NF26 RNA-Seq NF26 embryo Peshkin L et al. (2015) GSM1905652 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Readme.txt 73904 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [RiboZero] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 12 cycles amplification. 26555057 51556 SRP064686 WE - NF14 RNA-Seq NF14 embryo Peshkin L et al. (2015) GSM1905647 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Readme.txt 73904 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [RiboZero] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 12 cycles amplification. 26555057 51556 SRP064686 WE - NF8 RNA-Seq NF8 embryo Peshkin L et al. (2015) GSM1905642,GSM1905643 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Readme.txt 73904 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [RiboZero] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 12 cycles amplification. 26555057 51556 SRP064686 WE - mature egg RNA-Seq mature egg embryo Peshkin L et al. (2015) GSM1905637 RNA-Seq/Whole Embryo/unfertilized egg laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Readme.txt 73904 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [RiboZero] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 12 cycles amplification. 26555057 51556 SRP064686 WE - NF18 RNA-Seq NF18 embryo Peshkin L et al. (2015) GSM1905649 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Readme.txt 73904 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [RiboZero] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 12 cycles amplification. 26555057 51556 SRP064686 WE - NF6 RNA-Seq NF6 embryo Peshkin L et al. (2015) GSM1905639 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Readme.txt 73904 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [RiboZero] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 12 cycles amplification. 26555057 51556 SRP064686 WE - NF10 RNA-Seq NF10 embryo Peshkin L et al. (2015) GSM1905645 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Readme.txt 73904 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [RiboZero] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 12 cycles amplification. 26555057 51556 SRP064686 WE - NF16 RNA-Seq NF16 embryo Peshkin L et al. (2015) GSM1905648 RNA-Seq/Whole Embryo/Neurula NF13 to NF21 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Readme.txt 73904 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [RiboZero] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 12 cycles amplification. 26555057 51556 SRP064686 WE - NF29/30 RNA-Seq NF29/30 embryo Peshkin L et al. (2015) GSM1905653 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Readme.txt 73904 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [RiboZero] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 12 cycles amplification. 26555057 51556 SRP064686 WE - NF6.5 RNA-Seq NF6.5 embryo Peshkin L et al. (2015) GSM1905640 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Readme.txt 73904 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [RiboZero] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 12 cycles amplification. 26555057 51556 SRP064686 WE - NF7 RNA-Seq NF7 embryo Peshkin L et al. (2015) GSM1905641 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Readme.txt 73904 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [RiboZero] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 12 cycles amplification. 26555057 51556 SRP064686 WE - NF12 RNA-Seq NF12 embryo Peshkin L et al. (2015) GSM1905646 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Readme.txt 73904 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [RiboZero] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 12 cycles amplification. 26555057 51556 SRP064686 WE - NF23 RNA-Seq NF23 embryo Peshkin L et al. (2015) GSM1905651 RNA-Seq/Whole Embryo/Tailbud NF22 to NF44 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Readme.txt 73904 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [RiboZero] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 12 cycles amplification. 26555057 51556 SRP064686 WE - NF2 RNA-Seq NF2 embryo Peshkin L et al. (2015) GSM1905638 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Readme.txt 73904 Esther Pearl On the relationship of protein and mRNA dynamics in vertebrate embryonic development [RiboZero] A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 12 cycles amplification. 26555057 51556 SRP064686 WE - NF9 RNA-Seq NF9 embryo Peshkin L et al. (2015) GSM1905644 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE73904/XENLA_10.1/RNA-Seq/Readme.txt 74184 Charles Bradshaw Methylome analysis of deoxyadenosines in higher eukaryotes Here, we report that we detected N-6-methyl-deoxyadenosine (dA6m) not only in frog DNA, but also in other species including mouse and humans. Our meth Charles Bradshaw, Magdalena Koziol, Charles Bradshaw, George Allen, Ana Costa, Christian Frezza, John Gurdon Determining regions of deoxyadenosine methylation in M. musculus kidney and X. laevis fat, oviduct and testes 26689968 51669 SRP065025 m6A adipose tissue - adult MeDIP-seq adult adipose tissue Koziol MJ et al. (2016) GSM1912891,GSM1912892 MeDIP-seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/Readme.txt 74184 Charles Bradshaw Methylome analysis of deoxyadenosines in higher eukaryotes Here, we report that we detected N-6-methyl-deoxyadenosine (dA6m) not only in frog DNA, but also in other species including mouse and humans. Our meth Charles Bradshaw, Magdalena Koziol, Charles Bradshaw, George Allen, Ana Costa, Christian Frezza, John Gurdon Determining regions of deoxyadenosine methylation in M. musculus kidney and X. laevis fat, oviduct and testes 26689968 51669 SRP065025 m6A testis - adult MeDIP-seq adult testis Koziol MJ et al. (2016) GSM1912901,GSM1912902 MeDIP-seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/Readme.txt 74184 Charles Bradshaw Methylome analysis of deoxyadenosines in higher eukaryotes Here, we report that we detected N-6-methyl-deoxyadenosine (dA6m) not only in frog DNA, but also in other species including mouse and humans. Our meth Charles Bradshaw, Magdalena Koziol, Charles Bradshaw, George Allen, Ana Costa, Christian Frezza, John Gurdon Determining regions of deoxyadenosine methylation in M. musculus kidney and X. laevis fat, oviduct and testes 26689968 51669 SRP065025 m6A oviduct - adult MeDIP-seq adult oviduct Koziol MJ et al. (2016) GSM1912895,GSM1912896 MeDIP-seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/Readme.txt 74184 Charles Bradshaw Methylome analysis of deoxyadenosines in higher eukaryotes Here, we report that we detected N-6-methyl-deoxyadenosine (dA6m) not only in frog DNA, but also in other species including mouse and humans. Our meth Charles Bradshaw, Magdalena Koziol, Charles Bradshaw, George Allen, Ana Costa, Christian Frezza, John Gurdon Determining regions of deoxyadenosine methylation in M. musculus kidney and X. laevis fat, oviduct and testes 26689968 51669 SRP065025 adipose tissue - adult MeDIP-seq adult adipose tissue Koziol MJ et al. (2016) GSM1912889,GSM1912890 MeDIP-seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/Readme.txt 74184 Charles Bradshaw Methylome analysis of deoxyadenosines in higher eukaryotes Here, we report that we detected N-6-methyl-deoxyadenosine (dA6m) not only in frog DNA, but also in other species including mouse and humans. Our meth Charles Bradshaw, Magdalena Koziol, Charles Bradshaw, George Allen, Ana Costa, Christian Frezza, John Gurdon Determining regions of deoxyadenosine methylation in M. musculus kidney and X. laevis fat, oviduct and testes 26689968 51669 SRP065025 oviduct - adult MeDIP-seq adult oviduct Koziol MJ et al. (2016) GSM1912893,GSM1912894 MeDIP-seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/Readme.txt 74184 Charles Bradshaw Methylome analysis of deoxyadenosines in higher eukaryotes Here, we report that we detected N-6-methyl-deoxyadenosine (dA6m) not only in frog DNA, but also in other species including mouse and humans. Our meth Charles Bradshaw, Magdalena Koziol, Charles Bradshaw, George Allen, Ana Costa, Christian Frezza, John Gurdon Determining regions of deoxyadenosine methylation in M. musculus kidney and X. laevis fat, oviduct and testes 26689968 51669 SRP065025 testis - adult MeDIP-seq adult testis Koziol MJ et al. (2016) GSM1912897,GSM1912898 MeDIP-seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/Readme.txt 74184 Charles Bradshaw Methylome analysis of deoxyadenosines in higher eukaryotes Here, we report that we detected N-6-methyl-deoxyadenosine (dA6m) not only in frog DNA, but also in other species including mouse and humans. Our meth Charles Bradshaw, Magdalena Koziol, Charles Bradshaw, George Allen, Ana Costa, Christian Frezza, John Gurdon Determining regions of deoxyadenosine methylation in M. musculus kidney and X. laevis fat, oviduct and testes 26689968 51669 SRP065025 m6A* testis - adult MeDIP-seq adult testis Koziol MJ et al. (2016) GSM1912903,GSM1912904 MeDIP-seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/Readme.txt 74184 Charles Bradshaw Methylome analysis of deoxyadenosines in higher eukaryotes Here, we report that we detected N-6-methyl-deoxyadenosine (dA6m) not only in frog DNA, but also in other species including mouse and humans. Our meth Charles Bradshaw, Magdalena Koziol, Charles Bradshaw, George Allen, Ana Costa, Christian Frezza, John Gurdon Determining regions of deoxyadenosine methylation in M. musculus kidney and X. laevis fat, oviduct and testes 26689968 51669 SRP065025 Rabbit IgG testis - adult MeDIP-seq adult testis Koziol MJ et al. (2016) GSM1912899,GSM1912900 MeDIP-seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/Readme.txt 74184 Charles Bradshaw Methylome analysis of deoxyadenosines in higher eukaryotes Here, we report that we detected N-6-methyl-deoxyadenosine (dA6m) not only in frog DNA, but also in other species including mouse and humans. Our meth Charles Bradshaw, Magdalena Koziol, Charles Bradshaw, George Allen, Ana Costa, Christian Frezza, John Gurdon Determining regions of deoxyadenosine methylation in M. musculus kidney and X. laevis fat, oviduct and testes 26689968 51669 SRP065025 m6A** testis - adult MeDIP-seq adult testis Koziol MJ et al. (2016) GSM1912905,GSM1912906 MeDIP-seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Wait|Loader Wait ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74184/XENLA_10.1/MeDIP-seq/Readme.txt 74470 Leonid Peshkin Transcriptomic Insights into Genetic Diversity of Protein-Coding Genes in X. laevis We characterize the genetic diversity of Xenopus laevis strains using allele-specific RNA-seq data analysis and provide a catalogue of coding variatio Leonid Peshkin, Virginia Savova, Esther Pearl, Elvan Boke, Marko Horb, Sasha Gimelbrant We successfully performed natural mating of the two Xenopus strains: two reciprocal (BxJ, JxB) and two straight self (JxJ, BxB) crosses. We then collected tadpoles at a single developmental timepoint (stage NF 42), pooled ten tadpoles per cross, and isolated RNA from each pool. After RiboZero treatment, we constructed Illumina libraries, and performed RNAseq on HiSeq 2000, resulting in approximately 30 to 47 million reads per library with paired-end 100 base reads. 28283406 53166 SRP065480 WE B strain - NF42 RNA-Seq NF42 embryo Savova V et al. (2017) GSM1921263 RNA-Seq/Embryonic Tissues/Tailbud NF22 to NF44 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74470 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74470/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74470/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74470/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74470/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74470/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74470/XENLA_10.1/RNA-Seq/Readme.txt 74470 Leonid Peshkin Transcriptomic Insights into Genetic Diversity of Protein-Coding Genes in X. laevis We characterize the genetic diversity of Xenopus laevis strains using allele-specific RNA-seq data analysis and provide a catalogue of coding variatio Leonid Peshkin, Virginia Savova, Esther Pearl, Elvan Boke, Marko Horb, Sasha Gimelbrant We successfully performed natural mating of the two Xenopus strains: two reciprocal (BxJ, JxB) and two straight self (JxJ, BxB) crosses. We then collected tadpoles at a single developmental timepoint (stage NF 42), pooled ten tadpoles per cross, and isolated RNA from each pool. After RiboZero treatment, we constructed Illumina libraries, and performed RNAseq on HiSeq 2000, resulting in approximately 30 to 47 million reads per library with paired-end 100 base reads. 28283406 53166 SRP065480 WE B x J cross- NF42 RNA-Seq NF42 embryo Savova V et al. (2017) GSM1921264 RNA-Seq/Embryonic Tissues/Tailbud NF22 to NF44 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74470 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74470/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74470/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74470/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74470/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74470/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74470/XENLA_10.1/RNA-Seq/Readme.txt 74470 Leonid Peshkin Transcriptomic Insights into Genetic Diversity of Protein-Coding Genes in X. laevis We characterize the genetic diversity of Xenopus laevis strains using allele-specific RNA-seq data analysis and provide a catalogue of coding variatio Leonid Peshkin, Virginia Savova, Esther Pearl, Elvan Boke, Marko Horb, Sasha Gimelbrant We successfully performed natural mating of the two Xenopus strains: two reciprocal (BxJ, JxB) and two straight self (JxJ, BxB) crosses. We then collected tadpoles at a single developmental timepoint (stage NF 42), pooled ten tadpoles per cross, and isolated RNA from each pool. After RiboZero treatment, we constructed Illumina libraries, and performed RNAseq on HiSeq 2000, resulting in approximately 30 to 47 million reads per library with paired-end 100 base reads. 28283406 53166 SRP065480 WE J strain - NF42 RNA-Seq NF42 embryo Savova V et al. (2017) GSM1921265 RNA-Seq/Embryonic Tissues/Tailbud NF22 to NF44 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74470 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74470/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74470/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74470/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74470/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74470/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74470/XENLA_10.1/RNA-Seq/Readme.txt 74919 Zhihua Jiang Whole transcriptome target sequencing: profiling gene expression and alternative polyadenylation with one pipeline. We have developed a deep sequencing method called Whole Transcriptome Target Sequencing (WTTS), which sequences the 3’ ends of polyA+ RNA. This method Zhihua Jiang, Xiang Zhou, Rui Li, Jennifer Michal, Richard Harland A pooled total RNA sample derived from three male and three female adult frogs was used in seven trials to develop the WTTS assay. The same sample was sequenced using RNA-seq as control. Technical replicates of the same female adult frog were analyzed using the finalized WTTS library preparation method. Biological replicates, which included 10 embryo pools collected from two families at stages 6, 8, 11, 15 and 28 were subsequently analyzed to validate the finalized WTTS method. Six embryo samples collected at stages of 6, 8 and 11 were also sequenced using RNA-seq. Therefore, this submission involved a total of 26 libraries. 27098915 52200 SRP066064 WE - NF28 WTTS-Seq NF28 embryo Zhou X et al. (2016) GSM1937560,GSM1937561 WTTS-Seq/Whole Embryo/Tailbud NF22 to NF44 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Readme.txt 74919 Zhihua Jiang Whole transcriptome target sequencing: profiling gene expression and alternative polyadenylation with one pipeline. We have developed a deep sequencing method called Whole Transcriptome Target Sequencing (WTTS), which sequences the 3’ ends of polyA+ RNA. This method Zhihua Jiang, Xiang Zhou, Rui Li, Jennifer Michal, Richard Harland A pooled total RNA sample derived from three male and three female adult frogs was used in seven trials to develop the WTTS assay. The same sample was sequenced using RNA-seq as control. Technical replicates of the same female adult frog were analyzed using the finalized WTTS library preparation method. Biological replicates, which included 10 embryo pools collected from two families at stages 6, 8, 11, 15 and 28 were subsequently analyzed to validate the finalized WTTS method. Six embryo samples collected at stages of 6, 8 and 11 were also sequenced using RNA-seq. Therefore, this submission involved a total of 26 libraries. 27098915 52200 SRP066064 WE - NF11 RNA-Seq NF11 embryo Zhou X et al. (2016) GSM1937567,GSM1937568 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq/Readme.txt 74919 Zhihua Jiang Whole transcriptome target sequencing: profiling gene expression and alternative polyadenylation with one pipeline. We have developed a deep sequencing method called Whole Transcriptome Target Sequencing (WTTS), which sequences the 3’ ends of polyA+ RNA. This method Zhihua Jiang, Xiang Zhou, Rui Li, Jennifer Michal, Richard Harland A pooled total RNA sample derived from three male and three female adult frogs was used in seven trials to develop the WTTS assay. The same sample was sequenced using RNA-seq as control. Technical replicates of the same female adult frog were analyzed using the finalized WTTS library preparation method. Biological replicates, which included 10 embryo pools collected from two families at stages 6, 8, 11, 15 and 28 were subsequently analyzed to validate the finalized WTTS method. Six embryo samples collected at stages of 6, 8 and 11 were also sequenced using RNA-seq. Therefore, this submission involved a total of 26 libraries. 27098915 52200 SRP066064 WE - NF15 WTTS-Seq NF15 embryo Zhou X et al. (2016) GSM1937558,GSM1937559 WTTS-Seq/Whole Embryo/Neurula NF13 to NF21 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Readme.txt 74919 Zhihua Jiang Whole transcriptome target sequencing: profiling gene expression and alternative polyadenylation with one pipeline. We have developed a deep sequencing method called Whole Transcriptome Target Sequencing (WTTS), which sequences the 3’ ends of polyA+ RNA. This method Zhihua Jiang, Xiang Zhou, Rui Li, Jennifer Michal, Richard Harland A pooled total RNA sample derived from three male and three female adult frogs was used in seven trials to develop the WTTS assay. The same sample was sequenced using RNA-seq as control. Technical replicates of the same female adult frog were analyzed using the finalized WTTS library preparation method. Biological replicates, which included 10 embryo pools collected from two families at stages 6, 8, 11, 15 and 28 were subsequently analyzed to validate the finalized WTTS method. Six embryo samples collected at stages of 6, 8 and 11 were also sequenced using RNA-seq. Therefore, this submission involved a total of 26 libraries. 27098915 52200 SRP066064 WE - NF6 RNA-Seq NF6 embryo Zhou X et al. (2016) GSM1937563,GSM1937564 RNA-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq/Readme.txt 74919 Zhihua Jiang Whole transcriptome target sequencing: profiling gene expression and alternative polyadenylation with one pipeline. We have developed a deep sequencing method called Whole Transcriptome Target Sequencing (WTTS), which sequences the 3’ ends of polyA+ RNA. This method Zhihua Jiang, Xiang Zhou, Rui Li, Jennifer Michal, Richard Harland A pooled total RNA sample derived from three male and three female adult frogs was used in seven trials to develop the WTTS assay. The same sample was sequenced using RNA-seq as control. Technical replicates of the same female adult frog were analyzed using the finalized WTTS library preparation method. Biological replicates, which included 10 embryo pools collected from two families at stages 6, 8, 11, 15 and 28 were subsequently analyzed to validate the finalized WTTS method. Six embryo samples collected at stages of 6, 8 and 11 were also sequenced using RNA-seq. Therefore, this submission involved a total of 26 libraries. 27098915 52200 SRP066064 WE - NF6 (WTTS-Seq) WTTS-Seq NF6 embryo Zhou X et al. (2016) GSM1937552,GSM1937553 WTTS-Seq/Whole Embryo/Cleavage NF2- to NF6.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Readme.txt 74919 Zhihua Jiang Whole transcriptome target sequencing: profiling gene expression and alternative polyadenylation with one pipeline. We have developed a deep sequencing method called Whole Transcriptome Target Sequencing (WTTS), which sequences the 3’ ends of polyA+ RNA. This method Zhihua Jiang, Xiang Zhou, Rui Li, Jennifer Michal, Richard Harland A pooled total RNA sample derived from three male and three female adult frogs was used in seven trials to develop the WTTS assay. The same sample was sequenced using RNA-seq as control. Technical replicates of the same female adult frog were analyzed using the finalized WTTS library preparation method. Biological replicates, which included 10 embryo pools collected from two families at stages 6, 8, 11, 15 and 28 were subsequently analyzed to validate the finalized WTTS method. Six embryo samples collected at stages of 6, 8 and 11 were also sequenced using RNA-seq. Therefore, this submission involved a total of 26 libraries. 27098915 52200 SRP066064 WE - NF8 RNA-Seq NF8 embryo Zhou X et al. (2016) GSM1937565,GSM1937566 RNA-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq/Readme.txt 74919 Zhihua Jiang Whole transcriptome target sequencing: profiling gene expression and alternative polyadenylation with one pipeline. We have developed a deep sequencing method called Whole Transcriptome Target Sequencing (WTTS), which sequences the 3’ ends of polyA+ RNA. This method Zhihua Jiang, Xiang Zhou, Rui Li, Jennifer Michal, Richard Harland A pooled total RNA sample derived from three male and three female adult frogs was used in seven trials to develop the WTTS assay. The same sample was sequenced using RNA-seq as control. Technical replicates of the same female adult frog were analyzed using the finalized WTTS library preparation method. Biological replicates, which included 10 embryo pools collected from two families at stages 6, 8, 11, 15 and 28 were subsequently analyzed to validate the finalized WTTS method. Six embryo samples collected at stages of 6, 8 and 11 were also sequenced using RNA-seq. Therefore, this submission involved a total of 26 libraries. 27098915 52200 SRP066064 WE - adult RNA-Seq adult whole organism Zhou X et al. (2016) GSM1937562 RNA-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq/Readme.txt 74919 Zhihua Jiang Whole transcriptome target sequencing: profiling gene expression and alternative polyadenylation with one pipeline. We have developed a deep sequencing method called Whole Transcriptome Target Sequencing (WTTS), which sequences the 3’ ends of polyA+ RNA. This method Zhihua Jiang, Xiang Zhou, Rui Li, Jennifer Michal, Richard Harland A pooled total RNA sample derived from three male and three female adult frogs was used in seven trials to develop the WTTS assay. The same sample was sequenced using RNA-seq as control. Technical replicates of the same female adult frog were analyzed using the finalized WTTS library preparation method. Biological replicates, which included 10 embryo pools collected from two families at stages 6, 8, 11, 15 and 28 were subsequently analyzed to validate the finalized WTTS method. Six embryo samples collected at stages of 6, 8 and 11 were also sequenced using RNA-seq. Therefore, this submission involved a total of 26 libraries. 27098915 52200 SRP066064 WE - adult - Trial 2 WTTS-Seq adult whole organism Zhou X et al. (2016) GSM1937544 WTTS-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Readme.txt 74919 Zhihua Jiang Whole transcriptome target sequencing: profiling gene expression and alternative polyadenylation with one pipeline. We have developed a deep sequencing method called Whole Transcriptome Target Sequencing (WTTS), which sequences the 3’ ends of polyA+ RNA. This method Zhihua Jiang, Xiang Zhou, Rui Li, Jennifer Michal, Richard Harland A pooled total RNA sample derived from three male and three female adult frogs was used in seven trials to develop the WTTS assay. The same sample was sequenced using RNA-seq as control. Technical replicates of the same female adult frog were analyzed using the finalized WTTS library preparation method. Biological replicates, which included 10 embryo pools collected from two families at stages 6, 8, 11, 15 and 28 were subsequently analyzed to validate the finalized WTTS method. Six embryo samples collected at stages of 6, 8 and 11 were also sequenced using RNA-seq. Therefore, this submission involved a total of 26 libraries. 27098915 52200 SRP066064 WE - adult - Trial 5 WTTS-Seq adult whole organism Zhou X et al. (2016) GSM1937547 WTTS-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Readme.txt 74919 Zhihua Jiang Whole transcriptome target sequencing: profiling gene expression and alternative polyadenylation with one pipeline. We have developed a deep sequencing method called Whole Transcriptome Target Sequencing (WTTS), which sequences the 3’ ends of polyA+ RNA. This method Zhihua Jiang, Xiang Zhou, Rui Li, Jennifer Michal, Richard Harland A pooled total RNA sample derived from three male and three female adult frogs was used in seven trials to develop the WTTS assay. The same sample was sequenced using RNA-seq as control. Technical replicates of the same female adult frog were analyzed using the finalized WTTS library preparation method. Biological replicates, which included 10 embryo pools collected from two families at stages 6, 8, 11, 15 and 28 were subsequently analyzed to validate the finalized WTTS method. Six embryo samples collected at stages of 6, 8 and 11 were also sequenced using RNA-seq. Therefore, this submission involved a total of 26 libraries. 27098915 52200 SRP066064 WE - adult - Trial 7 WTTS-Seq adult whole organism Zhou X et al. (2016) GSM1937549 WTTS-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Readme.txt 74919 Zhihua Jiang Whole transcriptome target sequencing: profiling gene expression and alternative polyadenylation with one pipeline. We have developed a deep sequencing method called Whole Transcriptome Target Sequencing (WTTS), which sequences the 3’ ends of polyA+ RNA. This method Zhihua Jiang, Xiang Zhou, Rui Li, Jennifer Michal, Richard Harland A pooled total RNA sample derived from three male and three female adult frogs was used in seven trials to develop the WTTS assay. The same sample was sequenced using RNA-seq as control. Technical replicates of the same female adult frog were analyzed using the finalized WTTS library preparation method. Biological replicates, which included 10 embryo pools collected from two families at stages 6, 8, 11, 15 and 28 were subsequently analyzed to validate the finalized WTTS method. Six embryo samples collected at stages of 6, 8 and 11 were also sequenced using RNA-seq. Therefore, this submission involved a total of 26 libraries. 27098915 52200 SRP066064 WE (female) - adult WTTS-Seq adult whole organism Zhou X et al. (2016) GSM1937550,GSM1937551 WTTS-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Readme.txt 74919 Zhihua Jiang Whole transcriptome target sequencing: profiling gene expression and alternative polyadenylation with one pipeline. We have developed a deep sequencing method called Whole Transcriptome Target Sequencing (WTTS), which sequences the 3’ ends of polyA+ RNA. This method Zhihua Jiang, Xiang Zhou, Rui Li, Jennifer Michal, Richard Harland A pooled total RNA sample derived from three male and three female adult frogs was used in seven trials to develop the WTTS assay. The same sample was sequenced using RNA-seq as control. Technical replicates of the same female adult frog were analyzed using the finalized WTTS library preparation method. Biological replicates, which included 10 embryo pools collected from two families at stages 6, 8, 11, 15 and 28 were subsequently analyzed to validate the finalized WTTS method. Six embryo samples collected at stages of 6, 8 and 11 were also sequenced using RNA-seq. Therefore, this submission involved a total of 26 libraries. 27098915 52200 SRP066064 WE - adult - Trial 3 WTTS-Seq adult whole organism Zhou X et al. (2016) GSM1937545 WTTS-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Readme.txt 74919 Zhihua Jiang Whole transcriptome target sequencing: profiling gene expression and alternative polyadenylation with one pipeline. We have developed a deep sequencing method called Whole Transcriptome Target Sequencing (WTTS), which sequences the 3’ ends of polyA+ RNA. This method Zhihua Jiang, Xiang Zhou, Rui Li, Jennifer Michal, Richard Harland A pooled total RNA sample derived from three male and three female adult frogs was used in seven trials to develop the WTTS assay. The same sample was sequenced using RNA-seq as control. Technical replicates of the same female adult frog were analyzed using the finalized WTTS library preparation method. Biological replicates, which included 10 embryo pools collected from two families at stages 6, 8, 11, 15 and 28 were subsequently analyzed to validate the finalized WTTS method. Six embryo samples collected at stages of 6, 8 and 11 were also sequenced using RNA-seq. Therefore, this submission involved a total of 26 libraries. 27098915 52200 SRP066064 WE - adult - Trial 1 WTTS-Seq adult whole organism Zhou X et al. (2016) GSM1937543 WTTS-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Readme.txt 74919 Zhihua Jiang Whole transcriptome target sequencing: profiling gene expression and alternative polyadenylation with one pipeline. We have developed a deep sequencing method called Whole Transcriptome Target Sequencing (WTTS), which sequences the 3’ ends of polyA+ RNA. This method Zhihua Jiang, Xiang Zhou, Rui Li, Jennifer Michal, Richard Harland A pooled total RNA sample derived from three male and three female adult frogs was used in seven trials to develop the WTTS assay. The same sample was sequenced using RNA-seq as control. Technical replicates of the same female adult frog were analyzed using the finalized WTTS library preparation method. Biological replicates, which included 10 embryo pools collected from two families at stages 6, 8, 11, 15 and 28 were subsequently analyzed to validate the finalized WTTS method. Six embryo samples collected at stages of 6, 8 and 11 were also sequenced using RNA-seq. Therefore, this submission involved a total of 26 libraries. 27098915 52200 SRP066064 WE - adult - Trial 4 WTTS-Seq adult whole organism Zhou X et al. (2016) GSM1937546 WTTS-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Readme.txt 74919 Zhihua Jiang Whole transcriptome target sequencing: profiling gene expression and alternative polyadenylation with one pipeline. We have developed a deep sequencing method called Whole Transcriptome Target Sequencing (WTTS), which sequences the 3’ ends of polyA+ RNA. This method Zhihua Jiang, Xiang Zhou, Rui Li, Jennifer Michal, Richard Harland A pooled total RNA sample derived from three male and three female adult frogs was used in seven trials to develop the WTTS assay. The same sample was sequenced using RNA-seq as control. Technical replicates of the same female adult frog were analyzed using the finalized WTTS library preparation method. Biological replicates, which included 10 embryo pools collected from two families at stages 6, 8, 11, 15 and 28 were subsequently analyzed to validate the finalized WTTS method. Six embryo samples collected at stages of 6, 8 and 11 were also sequenced using RNA-seq. Therefore, this submission involved a total of 26 libraries. 27098915 52200 SRP066064 WE - adult - Trial 6 WTTS-Seq adult whole organism Zhou X et al. (2016) GSM1937548 WTTS-Seq/Adult Tissues tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Readme.txt 74919 Zhihua Jiang Whole transcriptome target sequencing: profiling gene expression and alternative polyadenylation with one pipeline. We have developed a deep sequencing method called Whole Transcriptome Target Sequencing (WTTS), which sequences the 3’ ends of polyA+ RNA. This method Zhihua Jiang, Xiang Zhou, Rui Li, Jennifer Michal, Richard Harland A pooled total RNA sample derived from three male and three female adult frogs was used in seven trials to develop the WTTS assay. The same sample was sequenced using RNA-seq as control. Technical replicates of the same female adult frog were analyzed using the finalized WTTS library preparation method. Biological replicates, which included 10 embryo pools collected from two families at stages 6, 8, 11, 15 and 28 were subsequently analyzed to validate the finalized WTTS method. Six embryo samples collected at stages of 6, 8 and 11 were also sequenced using RNA-seq. Therefore, this submission involved a total of 26 libraries. 27098915 52200 SRP066064 WE - NF11 (WTTS-Seq) WTTS-Seq NF11 embryo Zhou X et al. (2016) GSM1937556,GSM1937557 WTTS-Seq/Whole Embryo/Gastrula NF10 to NF12.5 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Readme.txt 74919 Zhihua Jiang Whole transcriptome target sequencing: profiling gene expression and alternative polyadenylation with one pipeline. We have developed a deep sequencing method called Whole Transcriptome Target Sequencing (WTTS), which sequences the 3’ ends of polyA+ RNA. This method Zhihua Jiang, Xiang Zhou, Rui Li, Jennifer Michal, Richard Harland A pooled total RNA sample derived from three male and three female adult frogs was used in seven trials to develop the WTTS assay. The same sample was sequenced using RNA-seq as control. Technical replicates of the same female adult frog were analyzed using the finalized WTTS library preparation method. Biological replicates, which included 10 embryo pools collected from two families at stages 6, 8, 11, 15 and 28 were subsequently analyzed to validate the finalized WTTS method. Six embryo samples collected at stages of 6, 8 and 11 were also sequenced using RNA-seq. Therefore, this submission involved a total of 26 libraries. 27098915 52200 SRP066064 WE - NF8 (WTTS-Seq) WTTS-Seq NF8 embryo Zhou X et al. (2016) GSM1937554,GSM1937555 WTTS-Seq/Whole Embryo/Blastula NF7 to NF9 tropicalis XT100 XENTR_10.0 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE74919/XENTR_10.0/WTTS-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 H3K4me2 spermatozoon - adult ChIP-Seq adult spermatozoon Teperek M et al. (2016) GSM1944474,GSM1944476,GSM1944478 ChIP-Seq/Epigenetic/H3K4me2 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 H3K4me3 spermatozoon - adult ChIP-Seq adult spermatozoon Teperek M et al. (2016) GSM1944479,GSM1944481,GSM1944483 ChIP-Seq/Epigenetic/H3K4me3 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 spermatid - adult (MNase-Seq) MNase-Seq adult spermatid Teperek M et al. (2016) GSM1944458,GSM1944459,GSM1944460 Chromatin Accessibility/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/MNase-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/MNase-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/MNase-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/MNase-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/MNase-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/MNase-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 spermatozoon - adult (MBD-Seq) MBD-Seq adult spermatozoon Teperek M et al. (2016) GSM1944464,GSM1944465,GSM1944466 MBD-Seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/MBD-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/MBD-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/MBD-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/MBD-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/MBD-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/MBD-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 input spermatid - adult H3K4me3 ChIP-Seq adult spermatid Teperek M et al. (2016) GSM1944496 None laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 H3K4me3 spermatid - adult (2) ChIP-Seq adult spermatid Teperek M et al. (2016) GSM1944498,GSM1944499 ChIP-Seq/Epigenetic/H3K4me3 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 WE + spermatid - NF10.5-11.5 (control) RNA-Seq NF10.5 embryo Teperek M et al. (2016) GSM1944426,GSM1944428,GSM1944429,GSM1944431,GSM1944435,GSM1944437,GSM1944438,GSM1944449,GSM1944450,GSM1944451,GSM1944453 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 WE + spermatid - NF10.5-11.5 (control) RNA-Seq NF10.5 embryo Teperek M et al. (2016) GSM1944426,GSM1944428,GSM1944429,GSM1944431,GSM1944435,GSM1944437,GSM1944438,GSM1944449,GSM1944450,GSM1944451,GSM1944453 Manipulations/mRNA Injection laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 WE + spermatid - NF10.5-11.5 (control) RNA-Seq NF10.5 embryo Teperek M et al. (2016) GSM1944426,GSM1944428,GSM1944429,GSM1944431,GSM1944435,GSM1944437,GSM1944438,GSM1944449,GSM1944450,GSM1944451,GSM1944453 Manipulations/Other laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 WE + kdm5b + spermatid - NF10.5-11.5 RNA-Seq NF10.5 embryo Teperek M et al. (2016) GSM1944425,GSM1944427,GSM1944430,GSM1944432,GSM1944433,GSM1944434,GSM1944436 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 WE + kdm5b + spermatid - NF10.5-11.5 RNA-Seq NF10.5 embryo Teperek M et al. (2016) GSM1944425,GSM1944427,GSM1944430,GSM1944432,GSM1944433,GSM1944434,GSM1944436 Manipulations/mRNA Injection laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 WE + kdm5b + spermatid - NF10.5-11.5 RNA-Seq NF10.5 embryo Teperek M et al. (2016) GSM1944425,GSM1944427,GSM1944430,GSM1944432,GSM1944433,GSM1944434,GSM1944436 Manipulations/Other laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 WE + UV + spermatid - NF10.5-11.5 (SE) RNA-Seq NF10.5 embryo Teperek M et al. (2016) GSM1944403,GSM1944405,GSM1944407,GSM1944409 Manipulations/Other laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 WE + UV + spermatid - NF10.5-11.5 (SE) RNA-Seq NF10.5 embryo Teperek M et al. (2016) GSM1944403,GSM1944405,GSM1944407,GSM1944409 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 WE + spermatozoon - NF10.5-11.5 (control) RNA-Seq NF10.5 embryo Teperek M et al. (2016) GSM1944440,GSM1944442,GSM1944444,GSM1944446 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 WE + spermatozoon - NF10.5-11.5 (control) RNA-Seq NF10.5 embryo Teperek M et al. (2016) GSM1944440,GSM1944442,GSM1944444,GSM1944446 Manipulations/mRNA Injection laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 WE + spermatozoon - NF10.5-11.5 (control) RNA-Seq NF10.5 embryo Teperek M et al. (2016) GSM1944440,GSM1944442,GSM1944444,GSM1944446 Manipulations/Other laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 input spermatid - adult ChIP-Seq adult spermatid Teperek M et al. (2016) GSM1944490,GSM1944492,GSM1944494 None laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 H3K4me2 spermatid - adult ChIP-Seq adult spermatid Teperek M et al. (2016) GSM1944491,GSM1944493,GSM1944495 ChIP-Seq/Epigenetic/H3K4me2 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 spermatid - adult RNA-Seq adult spermatid Teperek M et al. (2016) GSM1944414,GSM1944415,GSM1944416 RNA-Seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 input spermatozoon - adult ChIP-Seq adult spermatozoon Teperek M et al. (2016) GSM1944473,GSM1944475,GSM1944477 None laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 H3K9me3 spermatozoon - adult ChIP-Seq adult spermatozoon Teperek M et al. (2016) GSM1944484,GSM1944485,GSM1944486 ChIP-Seq/Epigenetic/H3K9me3 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 H3K27me3 spermatid - adult (2) ChIP-Seq adult spermatid Teperek M et al. (2016) GSM1944503,GSM1944505 ChIP-Seq/Epigenetic/H3K27me3 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 spermatid - adult (MBD-Seq) MBD-Seq adult spermatid Teperek M et al. (2016) GSM1944470,GSM1944471,GSM1944472 MBD-Seq/Adult Tissues laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/MBD-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/MBD-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/MBD-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/MBD-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/MBD-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/MBD-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 WE + kdm6b + spermatozoon - NF10.5-11.5 RNA-Seq NF10.5 embryo Teperek M et al. (2016) GSM1944439,GSM1944441,GSM1944443,GSM1944445 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 WE + kdm6b + spermatozoon - NF10.5-11.5 RNA-Seq NF10.5 embryo Teperek M et al. (2016) GSM1944439,GSM1944441,GSM1944443,GSM1944445 Manipulations/mRNA Injection laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 WE + kdm6b + spermatozoon - NF10.5-11.5 RNA-Seq NF10.5 embryo Teperek M et al. (2016) GSM1944439,GSM1944441,GSM1944443,GSM1944445 Manipulations/Other laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 WE + kdm6b + spermatid - NF10.5-11.5 RNA-Seq NF10.5 embryo Teperek M et al. (2016) GSM1944447,GSM1944448,GSM1944452,GSM1944454 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 WE + kdm6b + spermatid - NF10.5-11.5 RNA-Seq NF10.5 embryo Teperek M et al. (2016) GSM1944447,GSM1944448,GSM1944452,GSM1944454 Manipulations/mRNA Injection laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 WE + kdm6b + spermatid - NF10.5-11.5 RNA-Seq NF10.5 embryo Teperek M et al. (2016) GSM1944447,GSM1944448,GSM1944452,GSM1944454 Manipulations/Other laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 H3K9me3 spermatid - adult ChIP-Seq adult spermatid Teperek M et al. (2016) GSM1944500,GSM1944501,GSM1944502 ChIP-Seq/Epigenetic/H3K9me3 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 WE + UV + spermatozoon - NF10.5-11.5 (SE) RNA-Seq NF10.5 embryo Teperek M et al. (2016) GSM1944402,GSM1944404,GSM1944406,GSM1944408 Manipulations/Other laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 WE + UV + spermatozoon - NF10.5-11.5 (SE) RNA-Seq NF10.5 embryo Teperek M et al. (2016) GSM1944402,GSM1944404,GSM1944406,GSM1944408 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 WE + kdm5b + spermatozoon - NF10.5-11.5 RNA-Seq NF10.5 embryo Teperek M et al. (2016) GSM1944417,GSM1944419,GSM1944422,GSM1944424 RNA-Seq/Whole Embryo/Gastrula NF10 to NF12.5 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 WE + kdm5b + spermatozoon - NF10.5-11.5 RNA-Seq NF10.5 embryo Teperek M et al. (2016) GSM1944417,GSM1944419,GSM1944422,GSM1944424 Manipulations/mRNA Injection laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 WE + kdm5b + spermatozoon - NF10.5-11.5 RNA-Seq NF10.5 embryo Teperek M et al. (2016) GSM1944417,GSM1944419,GSM1944422,GSM1944424 Manipulations/Other laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/RNA-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 H3K27me3 spermatid - adult (1) ChIP-Seq adult spermatid Teperek M et al. (2016) GSM1944504 ChIP-Seq/Epigenetic/H3K27me3 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 H3K27me3 spermatozoon - adult (2) ChIP-Seq adult spermatozoon Teperek M et al. (2016) GSM1944487,GSM1944489 ChIP-Seq/Epigenetic/H3K27me3 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 H3K27me3 spermatozoon - adult (1) ChIP-Seq adult spermatozoon Teperek M et al. (2016) GSM1944488 ChIP-Seq/Epigenetic/H3K27me3 laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/BigWigs ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/ExpressionFiles ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/DE_Analysis ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Called_Peaks ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164/XENLA_10.1/ChIP-Seq/Readme.txt 75164 Charles Bradshaw Sperm is epigenetically programmed to regulate gene transcription in embryo Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in e Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin 27034506 53997 SRP066384 input spermatozoon - adult H3K4me3 ChIP-Seq adult spermatozoon Teperek M et al. (2016) GSM1944480,GSM1944482 None laevis XL101 XENLA_10.1 Curation Complete|PL Done|Loader Done ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75164 ftp.xenbaseturbofrog.org/Genomics/GEO/GSE75