Summary

Enhancers are genetic elements that regulate spatiotemporal gene expression. Enhancer function requires transcription factor (TF) binding and correlates with histone modifications (H3K27ac and H3K4me1). However, the extent to which TF binding and histone modifications can functionally define active enhancers remains unclear. We have combined chromatin immunoprecipitation with a massively parallel reporter assay to identify functional enhancers in human embryonic stem cells (hESCs) genome-wide in a quantitative unbiased manner. This website provides access to supplemental data for this resource.

Quick links

Enhancer Search

Find active enhancers near genes of interest.

Genome browser

Explore the functional enhancer repertoire of hESCs.

Enrichment analysis

Browse the complete results of all enrichment analyses.

Enhancer search

Dynamic search tool for active enhancers in the proximity of genes of interest.

Name	Description and link
Dynamic search tool	Search active enhancers in proximity of genes: Gene: Max. distance: 10kb50kb250kb Search
Full data download	Active enhancers and inactive peaks in proximity of gene promoters with additional annotations: 10kb window, 50kb window, 250kb window

Genome browser tracks

ChIP-seq, DNA-seq, and RNA-seq data for visualization as genome browser tracks. Related to Figure 1, Figure 4, and Figure 7 of the paper.

Name	Description and link
Genome browser (GRCh37/hg19)	Genome browser track hub (temporary link): https://www.biomedical-sequencing.at/bocklab/papers/barakat2018/hub-starr.txt Direct link: Open in UCSC genome browser (USA), Open in UCSC genome browser (Europe), Open in Ensembl genome browser
Selected tracks (GRCh37/hg19)	ChIP-seq peaks: OCT4 peaks (BED), NANOG peaks (BED), H3K27ac peaks (BED), H3K4me1 peaks (BED) Enhancer activity: H9 primed (BED), H9 primed (BigBed), H9 naive (BED), H9 naive (BigBed), Super-enhancers: H9 primed (BED), H9 primed (BigBed), H9 naive (BED), H9 naive (BigBed),
Screenshots	Selection of screenshots: PDF
Tutorials	UCSC: Using genome browser track hubs Ensembl: Adding track hubs

Analysis results

Additional analysis results.

Name	Description and link
Enhancer neighbourhood of primed/naive genes	TSS+/-100kb: Higher expression in primed, higher expression in naive

Data and links

Links to raw data archives and related resources.

Name	Description and link
GEO	GSE99631
BioProject	PRJNA389108
SRA	SRP108517 (ChIP-seq) SRP108518 (islotated plasmids) SRP108519 (plasmids) SRP108520 (RNA-eq)
Embryonic Stem Cell Biology	Homepage: Embryonic Stem Cell Biology Lab @ SCRM, Edinburgh
Medical Epigenomics	Homepage: Medical Epigenomics Lab @ CeMM, Vienna
Related publications:	LOLA: Software used for region overlap enrichment analysis used throughout our paper. Homepage GitHub Bioinformatics (Open Access)

Citation

If you use this resource in your research, please cite:

Barakat TS^*, Halbritter F^*, Zhang M, Rendeiro AF, Bock C & Chambers I. (2018) Functional dissection of the enhancer repertoire in human embryonic stem cells. Cell Stem Cell,
doi: 10.1016/j.stem.2018.06.014