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

Table 1 Datasets used in the integrative modeling

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, 33–35]
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]

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.

ISSN: 1471-2164