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ChIP-seq, RNA-seq and ATAC-seq obtained from endoderm differentiation of human Embryonic Stem Cells (hESCs) synchronised in G1 phase of the cell cycle using the FUCCI reporter system

All genome-wide maps of histone modifications (H3K4me3, H3K27me3, H3K36me3, H3K4me1, H3K27ac), DNA accessibility, and RNA expression are freely available in this web portal through a genome browser or via direct download.

Raw sequencing data have been deposited in ArrayExpress with accessions E-MTAB-9276, E-MTAB-9194 and E-MTAB-9124.

Visualise Data in Biodalliance Genome Browser

Click on '+', select the tab 'Definitive Endoderm', and choose datasets for visualisation.

You can enter a location or gene name (e.g. SOX17).

Download Data

ChIP-seq processed data


Super-enhancers at each time point, ranked by expression of nearby genes.

Super-enhancers 0h (434)

Super-enhancers 12h (707)

Super-enhancers 24h (637)

Super-enhancers 36h (2362)

Super-enhancers 48h (1335)

Super-enhancers 72h (708)

Normalised ChIP-seq Signal (bigWig format)

H3K4me3 0h (Replicate 1)

H3K4me3 0h (Replicate 2)

H3K4me3 12h (Replicate 1)

H3K4me3 12h (Replicate 2)

H3K4me3 24h (Replicate 1)

H3K4me3 24h (Replicate 2)

H3K4me3 36h (Replicate 1)

H3K4me3 48h (Replicate 1)

H3K4me3 48h (Replicate 2)

H3K4me3 72h (Replicate 1)

H3K4me3 72h (Replicate 2)

H3K27me3 0h (Replicate 1)

H3K27me3 0h (Replicate 2)

H3K27me3 12h (Replicate 1)

H3K27me3 12h (Replicate 2)

H3K27me3 24h (Replicate 1)

H3K27me3 24h (Replicate 2)

H3K27me3 36h (Replicate 1 - failed)

H3K27me3 48h (Replicate 1)

H3K27me3 48h (Replicate 2)

H3K27me3 72h (Replicate 1)

H3K27me3 72h (Replicate 2)

H3K27ac 0h (Replicate 1)

H3K27ac 0h (Replicate 2)

H3K27ac 12h (Replicate 1)

H3K27ac 12h (Replicate 2)

H3K27ac 24h (Replicate 1)

H3K27ac 24h (Replicate 2)

H3K27ac 36h (Replicate 1)

H3K27ac 48h (Replicate 1)

H3K27ac 48h (Replicate 2)

H3K27ac 72h (Replicate 1)

H3K27ac 72h (Replicate 2)

H3K4me1 0h (Replicate 1)

H3K4me1 0h (Replicate 2)

H3K4me1 12h (Replicate 1)

H3K4me1 12h (Replicate 2)

H3K4me1 24h (Replicate 1)

H3K4me1 24h (Replicate 2)

H3K4me1 36h (Replicate 1)

H3K4me1 48h (Replicate 1)

H3K4me1 48h (Replicate 2)

H3K4me1 72h (Replicate 1)

H3K4me1 72h (Replicate 2)

H3K36me3 0h (Replicate 1)

H3K36me3 0h (Replicate 2)

H3K36me3 12h (Replicate 1)

H3K36me3 12h (Replicate 2)

H3K36me3 24h (Replicate 1)

H3K36me3 24h (Replicate 2)

H3K36me3 36h (Replicate 1)

H3K36me3 48h (Replicate 1)

H3K36me3 48h (Replicate 2)

H3K36me3 72h (Replicate 1)

H3K36me3 72h (Replicate 2)

Input control for H3K4me3, H3K27ac, H3K4me1, H3K36me3 at 0h, 12h, 24h, 48, 72h (Replicates 1-2)

Input control for H3K4me3, H3K27ac, H3K4me1, H3K36me3 at 0h, 12h, 24h, 48, 72h (Replicates 1-2)

Input control for H3K27me3 0h, 12h, 24h, 48h, 72h (Replicate 1)

Input control for H3K27me3 0h, 12h, 24h, 48h, 72h (Replicate 2)

Input control for all samples at 36h (Replicate 1)

Peak calling

Reproducible ChIP-seq peaks at each time-point (BED and BigBed format)

Differential ChIP-seq

Differential ChIP-seq regions reported by diffReps v1.55.6

ATAC-seq processed data

Normalised ATAC-seq Signal (bigWig format)

0h (Replicate 1 - ID: ATAC1)

0h (Replicate 2 - ID: ATAC2)

12h (Replicate 1 - ID: ATAC9)

12h (Replicate 2 - ID: ATAC10)

24h (Replicate 1 - ID: ATAC11)

24h (Replicate 2 - ID: ATAC12)

36h (Replicate 1 - ID: ATAC21)

36h (Replicate 2 - ID: ATAC22)

48h (Replicate 1 - ID: ATAC13)

48h (Replicate 2 - ID: ATAC14)

72h (Replicate 1 - ID: ATAC15)

72h (Replicate 2 - ID: ATAC16)

Deproteinized (naked DNA) control (ID: ATAC17)

Consolidated Open Chromatin Regions (ATAC-seq peaks)

Consolidated (merged) list of open chromatin regions across all time-points

TF footprints (Wellington)

Transcription Factor Footprints at each time-point (FDR 0.1)

Differential TF footprints (Wellington_bootstrap)

Differential Transcription Factor Footprints (FDR 0.05) between consecutive time-points

Tn5 insertion frequencies for every base

Obtained with with the tool NucleoATAC over merged replicates, and then converted to bigwig:

pyatac ins --bam BAMFILE

insertion frequencies 0h

insertion frequencies 12h

insertion frequencies 24h

insertion frequencies 36h

insertion frequencies 48h

insertion frequencies 72h

insertion frequencies Control

Differential Open Chromatin Regions

Differential Open Chromatin regions (Fold-change 2, adjusted-P 1e-4)

Raw peak calling with JAMM and Irreproducible Discovery Rate between replicates

Peak calling on each sample and reproducible peaks (IDR 0.05)

RNA-seq processed data

Normalised RNA-seq Signal (bigWig format)

0h (Replicate 1)

0h (Replicate 2)

0h (Replicate 3)

12h (Replicate 1)

12h (Replicate 2)

12h (Replicate 3)

24h (Replicate 1)

24h (Replicate 2)

24h (Replicate 3)

36h (Replicate 1)

36h (Replicate 2)

36h (Replicate 3)

48h (Replicate 1)

48h (Replicate 2)

48h (Replicate 3)

60h (Replicate 1)

60h (Replicate 2)

60h (Replicate 3)

72h (Replicate 1)

72h (Replicate 2)

72h (Replicate 3)

Gene read counts (Unnormalized)

Read counts (GRCh38.76)

Differential gene expression (DESEQ2)

Differential gene expression analyses between consecutive time-points

TF gene expression patterns after k-means clustering

Gene expression clusters


Madrigal P, et al. Epigenetic and transcriptional regulations prime cell fate before cell division during human pluripotent stem cell differentiation.

Wellcome - MRC Cambridge Stem Cell Institute

Wellcome Sanger Institute