Predicting enhancers in mammalian genomes using supervised hidden Markov models

BMC Bioinformatics

Table 2 Data sources. Accession numbers containing GSE were obtained from GEO [59–62], those starting with ENC from ENCODE

Cell type	Experiment	Target	Accession	Format
ESC E14	ATAC-seq	-	GSE120376	fastq
	ChIP-seq	H3K27ac	GSE120376	fastq
		H3K4me1	GSE120376	fastq
		H3K4me3	GSE120376	fastq
		Nanog	GSE11431	fastq
		Oct4	GSE11431	fastq
		Sox2	GSE11431	fastq
		CTCF	GSE29184	fastq
		p300	GSE29184	fastq
		Pol II	GSE29184	fastq
	MeDIP-seq	-	GSE3859	fastq
liver E12.5	ATAC-seq	-	ENCSR302LIV	bam
	ChIP-seq	H3K27ac	ENCSR136GMT	bam
		H3K4me1	ENCSR770OXU	bam
		H3K4me3	ENCSR471SJG	bam
liver E14.5	ATAC-seq	-	ENCSR032HKE	fastq
	ChIP-seq	H3K27ac	ENCSR075SNV	bam
		H3K4me1	ENCSR234ISO	bam
		H3K4me3	ENCSR433ESG	bam
lung E14.5	ATAC-seq	-	ENCSR335VJW	fastq
	ChIP-seq	H3K27ac	ENCSR452WYC	bam
		H3K4me1	ENCSR825OWH	bam
		H3K4me3	ENCSR839WFP	bam
lung E16.5	ATAC-seq	-	ENCSR627OCR	fastq
	ChIP-seq	H3K27ac	ENCSR140UEX	bam
		H3K4me1	ENCSR387YSD	bam
		H3K4me3	ENCSR295PFM	bam

ISSN: 1471-2105