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Table 1 Datasets used in the integrative modeling

From: Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features

Data Data Type Cell Line Purpose Accession Ref
RNA RNA-Seq V6.5 cells Feature GSE20851 [32]
Histone modifications (H3, H3K4me1, H3K4me2, H3K4me3, H3K36me3, H4K20me3, H3K27me3, H3K9me3) and RNAPII ChIP-Seq V6.5 cells Feature GSE11172 GSE12241 [29]
RNAPII-ser2, RNAPII-ser5 ChIP-Seq V6.5 cells Feature GSE20530 [30]
SMC1A, SMC3, MED12, MED1, NIPBL ChIP-Seq V6.5 cells Feature GSE22562 [22]
p300 ChIP-Seq E14 cells Feature GSE11431 [5]
CTCF ChIP-Seq V6.5 cells Feature GSE18699 [28]
CpG islands, GC content, SNP, repeat regions and PhastCons most conserved regions BED files -- Feature mm9 [31, 3335]
OCT4, SOX2, NANOG, MYC, MYCN ChIP-Seq E14 cells Training sets GSE11431 [5]
KLF4, STAT3, SMAD1, E2F1, TFCP2L1, ZFX, ESRRB ChIP-Seq E14 cells MTL analysis GSE11431 [5]
  1. The RNA-Seq, ChIP-Seq and genomic feature data sets used in the study are listed and cited in the table. Columns represent the cell line of mouse ES cells used (Cell Line), the usage of the data (Purpose), the NCBI GEO accession number (Accession), and the reference in which the data was generated (Ref). MTL: multiple transcription factor bound loci.