GSE: GSE56169 GSE Title: E2a is necessary for Smad2/3 dependent transcription and the direct repression of lefty Xenbase Article Id: XB-ART-50519 Pubmed Id: 25669884 FTP Location: ftp://xenbaseturbofrog.org/genomics/GEO/GSE56169/XENTR_10.0/ChIP-Seq/ NGS Data: ChIP-Seq Folder Descriptions: BigWigs: .bw files in the folder represent binary format of mapped read intensity in the genome. These files can be used for Visualization purposes. Called_Peaks: Peak calls per sample are obtained using MACS2 Track Track Name GSM1357034_1689.bw Smad2/3 WE + tcf3 MO - NF10.5 GSM1357032_1692_narrowPeaks.bed Smad2/3 WE - NF10.5 GSM1357037_1691_narrowPeaks.bed input WE - NF10.5 GSM1357034_1689_narrowPeaks.bed Smad2/3 WE + tcf3 MO - NF10.5 GSM1357032_1692.bw Smad2/3 WE - NF10.5 GSM1357037_1691.bw input WE - NF10.5 GSE: GSE56169 GSE Title: E2a is necessary for Smad2/3 dependent transcription and the direct repression of lefty Xenbase Article Id: XB-ART-50519 Pubmed Id: 25669884 FTP Location: ftp://xenbaseturbofrog.org/genomics/GEO/GSE56169/XENTR_10.0/RNA-Seq/ NGS Data: RNA-Seq Folder Descriptions: BigWigs: .bw files in the folder represent binary format of mapped read intensity in the genome. These files can be used for Visualization purposes. ExpressionFiles: Genes_TPM_Matrix.txt and Genes_Counts_Matrix.txt provide TPM and raw counts of genes across samples resepctively DE_Analysis: Differential Expression results between conditions. LogFC and FDR values can used to obtain differentially expressed genes Track Track Name GSM1357039_1690.bw WE - NF10.5 GSM1357041_1688.bw WE + tcf3 MO - NF10.5 GSE: GSE67974 GSE Title: Embryonic transcription is controlled by maternally defined chromatin state Xenbase Article Id: XB-ART-51677 Pubmed Id: 26679111 FTP Location: ftp://xenbaseturbofrog.org/genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ NGS Data: ChIP-Seq Folder Descriptions: BigWigs: .bw files in the folder represent binary format of mapped read intensity in the genome. These files can be used for Visualization purposes. Called_Peaks: Peak calls per sample are obtained using MACS2 Track Track Name GSM1659906_1397.bw H3K4me3 WE - NF12 GSM1659919_1392.bw H3K36me3 WE - NF29/30 GSM1659901_1379_broadPeaks.bed H3K4me3 WE - NF8 GSM1659911_1359.bw H3K9ac WE - NF10.5 GSM1659947_1411.bw H3K9me3 WE - NF12 GSM1659954_1398_broadPeaks.bed H4K20me3 WE - NF29/30 GSM1659935_1370.bw H3K27me3 WE + alpha amanitin - NF11 GSM1659949_1374_broadPeaks.bed H3K9me3 WE - NF29/30 GSM1659907_1363_broadPeaks.bed H3K4me3 WE - NF16 GSM1659933_1403.bw H3K27me3 WE - NF9 GSM1659909_1400.bw H3K9ac WE - NF8 GSM1659939_1424_broadPeaks.bed H3K27me3 WE - NF29/30 GSM1659937_1414_broadPeaks.bed H3K27me3 WE - NF12 GSM1659939_1424.bw H3K27me3 WE - NF29/30 GSM1659898_1422.bw H3K4me1 WE - NF12 GSM1659953_1421_broadPeaks.bed H4K20me3 WE - NF16 GSM1659910_1408_broadPeaks.bed H3K9ac WE - NF9 GSM1659917_1381_broadPeaks.bed H3K36me3 WE - NF12 GSM1659916_1368.bw H3K36me3 WE - NF10.5 GSM1659896_1410_broadPeaks.bed H3K4me1 WE - NF9 GSM1659912_1367.bw H3K9ac WE - NF12 GSM1659952_1405.bw H4K20me3 WE - NF12 GSM1659951_1416_broadPeaks.bed H4K20me3 WE - NF10.5 GSM1659903_1419_broadPeaks.bed H3K4me3 WE - NF10.5 GSM1659940_1390_broadPeaks.bed H3K9me2 WE - NF9 GSM1659897_1420_broadPeaks.bed H3K4me1 WE - NF10.5 GSM1659934_1409_broadPeaks.bed H3K27me3 WE - NF10.5 GSM1659944_1395_broadPeaks.bed H3K9me2 WE - NF29/30 GSM1659951_1416.bw H4K20me3 WE - NF10.5 GSM1659899_1417_broadPeaks.bed H3K4me1 WE - NF16 GSM1659934_1409.bw H3K27me3 WE - NF10.5 GSM1659902_1364.bw H3K4me3 WE - NF9 GSM1659916_1368_broadPeaks.bed H3K36me3 WE - NF10.5 GSM1659905_1384_broadPeaks.bed H3K4me3 WE - NF11 GSM1659945_1385.bw H3K9me3 WE - NF9 GSM1659949_1374.bw H3K9me3 WE - NF29/30 GSM1659903_1419.bw H3K4me3 WE - NF10.5 GSM1659944_1395.bw H3K9me2 WE - NF29/30 GSM1659935_1370_broadPeaks.bed H3K27me3 WE + alpha amanitin - NF11 GSM1659906_1397_broadPeaks.bed H3K4me3 WE - NF12 GSM1659908_1371_broadPeaks.bed H3K4me3 WE - NF29/30 GSM1659899_1417.bw H3K4me1 WE - NF16 GSM1659950_1399_broadPeaks.bed H4K20me3 WE - NF9 GSM1659946_1423_broadPeaks.bed H3K9me3 WE - NF10.5 GSM1659898_1422_broadPeaks.bed H3K4me1 WE - NF12 GSM1659905_1384.bw H3K4me3 WE - NF11 GSM1659919_1392_broadPeaks.bed H3K36me3 WE - NF29/30 GSM1659943_1394.bw H3K9me2 WE - NF16 GSM1659937_1414.bw H3K27me3 WE - NF12 GSM1659904_1380.bw H3K4me3 WE + alpha amanitin - NF11 GSM1659913_1389_broadPeaks.bed H3K9ac WE - NF16 GSM1659942_1369_broadPeaks.bed H3K9me2 WE - NF12 GSM1659918_1362_broadPeaks.bed H3K36me3 WE - NF16 GSM1659941_1372.bw H3K9me2 WE - NF10.5 GSM1659953_1421.bw H4K20me3 WE - NF16 GSM1659900_1366.bw H3K4me1 WE - NF29/30 GSM1659915_1373.bw H3K36me3 WE - NF9 GSM1659915_1373_broadPeaks.bed H3K36me3 WE - NF9 GSM1659941_1372_broadPeaks.bed H3K9me2 WE - NF10.5 GSM1659910_1408.bw H3K9ac WE - NF9 GSM1659900_1366_broadPeaks.bed H3K4me1 WE - NF29/30 GSM1659940_1390.bw H3K9me2 WE - NF9 GSM1659908_1371.bw H3K4me3 WE - NF29/30 GSM1659918_1362.bw H3K36me3 WE - NF16 GSM1659902_1364_broadPeaks.bed H3K4me3 WE - NF9 GSM1659901_1379.bw H3K4me3 WE - NF8 GSM1659947_1411_broadPeaks.bed H3K9me3 WE - NF12 GSM1659936_1382_broadPeaks.bed H3K27me3 WE - NF11 GSM1659933_1403_broadPeaks.bed H3K27me3 WE - NF9 GSM1659950_1399.bw H4K20me3 WE - NF9 GSM1659948_1406_broadPeaks.bed H3K9me3 WE - NF16 GSM1659914_1412.bw H3K9ac WE - NF29/30 GSM1659942_1369.bw H3K9me2 WE - NF12 GSM1659952_1405_broadPeaks.bed H4K20me3 WE - NF12 GSM1659896_1410.bw H3K4me1 WE - NF9 GSM1659954_1398.bw H4K20me3 WE - NF29/30 GSM1659945_1385_broadPeaks.bed H3K9me3 WE - NF9 GSM1659936_1382.bw H3K27me3 WE - NF11 GSM1659946_1423.bw H3K9me3 WE - NF10.5 GSM1659913_1389.bw H3K9ac WE - NF16 GSM1659911_1359_broadPeaks.bed H3K9ac WE - NF10.5 GSM1659943_1394_broadPeaks.bed H3K9me2 WE - NF16 GSM1659904_1380_broadPeaks.bed H3K4me3 WE + alpha amanitin - NF11 GSM1659948_1406.bw H3K9me3 WE - NF16 GSM1659932_1404_broadPeaks.bed H3K27me3 WE - NF8 GSM1659914_1412_broadPeaks.bed H3K9ac WE - NF29/30 GSM1659938_1407.bw H3K27me3 WE - NF16 GSM1659909_1400_broadPeaks.bed H3K9ac WE - NF8 GSM1659917_1381.bw H3K36me3 WE - NF12 GSM1659897_1420.bw H3K4me1 WE - NF10.5 GSM1659912_1367_broadPeaks.bed H3K9ac WE - NF12 GSM1659938_1407_broadPeaks.bed H3K27me3 WE - NF16 GSM1659907_1363.bw H3K4me3 WE - NF16 GSM1659932_1404.bw H3K27me3 WE - NF8 GSE: GSE67974 GSE Title: Embryonic transcription is controlled by maternally defined chromatin state Xenbase Article Id: XB-ART-51677 Pubmed Id: 26679111 FTP Location: ftp://xenbaseturbofrog.org/genomics/GEO/GSE67974/XENTR_10.0/ChIP-Seq/ NGS Data: ChIP-Seq Folder Descriptions: BigWigs: .bw files in the folder represent binary format of mapped read intensity in the genome. These files can be used for Visualization purposes. Called_Peaks: Peak calls per sample are obtained using MACS2 Track Track Name GSM1659931_1413.bw Pol II WE - NF29/30 GSM1659925_1386_narrowPeaks.bed ep300 WE - NF16 GSM1659922_1391.bw ep300 WE + alpha amanitin - NF11 GSM1974229_1415_narrowPeaks.bed Pol II WE + alpha amanitin - NF11 GSM1659923_1396_narrowPeaks.bed ep300 WE - NF11 GSM1659924_1388_narrowPeaks.bed ep300 WE - NF12 GSM1659921_1387_narrowPeaks.bed ep300 WE - NF10.5 GSM1659930_1376_narrowPeaks.bed Pol II WE - NF16 GSM1974229_1415.bw Pol II WE + alpha amanitin - NF11 GSM1659922_1391_narrowPeaks.bed ep300 WE + alpha amanitin - NF11 GSM1659927_1361.bw Pol II WE - NF9 GSM1659921_1387.bw ep300 WE - NF10.5 GSM1659928_1418_narrowPeaks.bed Pol II WE - NF10.5 GSM1659920_1377.bw ep300 WE - NF9 GSM1659920_1377_narrowPeaks.bed ep300 WE - NF9 GSM1974230_1360_narrowPeaks.bed Pol II WE - NF11 GSM1659929_1401_narrowPeaks.bed Pol II WE - NF12 GSM1659926_1378.bw ep300 WE - NF29/30 GSM1974230_1360.bw Pol II WE - NF11 GSM1659930_1376.bw Pol II WE - NF16 GSM1659927_1361_narrowPeaks.bed Pol II WE - NF9 GSM1659928_1418.bw Pol II WE - NF10.5 GSM1659929_1401.bw Pol II WE - NF12 GSM1659924_1388.bw ep300 WE - NF12 GSM1659926_1378_narrowPeaks.bed ep300 WE - NF29/30 GSM1659923_1396.bw ep300 WE - NF11 GSM1659931_1413_narrowPeaks.bed Pol II WE - NF29/30 GSM1659925_1386.bw ep300 WE - NF16 GSE: GSE67974 GSE Title: Embryonic transcription is controlled by maternally defined chromatin state Xenbase Article Id: XB-ART-51677 Pubmed Id: 26679111 FTP Location: ftp://xenbaseturbofrog.org/genomics/GEO/GSE67974/XENTR_10.0/RNA-Seq/ NGS Data: RNA-Seq Folder Descriptions: BigWigs: .bw files in the folder represent binary format of mapped read intensity in the genome. These files can be used for Visualization purposes. ExpressionFiles: Genes_TPM_Matrix.txt and Genes_Counts_Matrix.txt provide TPM and raw counts of genes across samples resepctively DE_Analysis: Differential Expression results between conditions. LogFC and FDR values can used to obtain differentially expressed genes Track Track Name GSM1974232_1375.bw WE - NF11 GSM1974231_1365.bw WE + alpha amanitin - NF11 GSE: GSE72657 GSE Title: Tissue- and stage-specific cellular context regulates Wnt target gene expression subsequent to β-catenin recruitment Xenbase Article Id: XB-ART-52077 Pubmed Id: 27068107 FTP Location: ftp://xenbaseturbofrog.org/genomics/GEO/GSE72657/XENTR_10.0/ChIP-Seq/ NGS Data: ChIP-Seq Folder Descriptions: BigWigs: .bw files in the folder represent binary format of mapped read intensity in the genome. These files can be used for Visualization purposes. Called_Peaks: Peak calls per sample are obtained using MACS2 Track Track Name GSM1867400_1687_narrowPeaks.bed beta Catenin WE - NF10.25 GSM1867401_1683_narrowPeaks.bed input WE - NF10.25 GSM1867401_1683.bw input WE - NF10.25 GSM1867400_1687.bw beta Catenin WE - NF10.25 GSE: GSE72657 GSE Title: Tissue- and stage-specific cellular context regulates Wnt target gene expression subsequent to β-catenin recruitment Xenbase Article Id: XB-ART-52077 Pubmed Id: 27068107 FTP Location: ftp://xenbaseturbofrog.org/genomics/GEO/GSE72657/XENTR_10.0/RNA-Seq/ NGS Data: RNA-Seq Folder Descriptions: BigWigs: .bw files in the folder represent binary format of mapped read intensity in the genome. These files can be used for Visualization purposes. ExpressionFiles: Genes_TPM_Matrix.txt and Genes_Counts_Matrix.txt provide TPM and raw counts of genes across samples resepctively DE_Analysis: Differential Expression results between conditions. LogFC and FDR values can used to obtain differentially expressed genes Track Track Name GSM1867403_1684.bw WE + hbg1 MO - NF10.25 GSM1867405_1682.bw WE + wnt8a MO + wnt8a - NF10.25 GSM1867402_1685.bw WE - NF10.25 GSM1867404_1686.bw WE + wnt8a MO - NF10.25 GSE: GSE74919 GSE Title: Whole transcriptome target sequencing Xenbase Article Id: XB-ART-52200 Pubmed Id: 27098915 FTP Location: ftp://xenbaseturbofrog.org/genomics/GEO/GSE74919/XENTR_10.0/RNA-Seq/ NGS Data: RNA-Seq Folder Descriptions: BigWigs: .bw files in the folder represent binary format of mapped read intensity in the genome. These files can be used for Visualization purposes. ExpressionFiles: Genes_TPM_Matrix.txt and Genes_Counts_Matrix.txt provide TPM and raw counts of genes across samples resepctively DE_Analysis: Differential Expression results between conditions. LogFC and FDR values can used to obtain differentially expressed genes Track Track Name GSM1937567_1712.bw WE - NF11 GSM1937565_1714.bw WE - NF8 GSM1937562_1716.bw WE - adult GSM1937563_1710.bw WE - NF6