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| Status |
Public on Oct 21, 2021 |
| Title |
Genome-wide quantitative functional enhancer map of mESCs, in the pluripotent state and after induced differentiation |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Precise spatiotemporally regulated gene expression is pivotal for cell homeostasis, cell differentiation and during development. Gene expression networks are tightly regulated by transcription factors (TF) and their targeted regulatory genomic elements (enhancers), which are known to correlate with specific histone modifications. However, the ultimate prerequisites, which determine functionally active enhancers, remain unclear. To elucidate the regulatory landscape of murine ESCs, a massively parallel reporter assay, based on STARR-seq (Self-Transcribing Active Regulatory Region sequencing), assessing genomic fragments prepared from accessible chromatin, (FAIRE-STARR-seq) has been applied. Thus, a genome-wide quantitative map of functional mESC enhancers in naive state and after retinoic acid (RA)-induced differentiation was generated. To investigate sequence features associated with RA-mediated inducibility of enhancers bound by retinoic acid receptor alpha (RARα), the main receptor for RA, genomic binding sites of RARα have been determined.
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| Overall design |
mESCs, in the pluripotent state or after induced differentiation, were assessed for genome-wide changes enhancer activity by FAIRE-STARR-seq. Additionally, RARα genomic binding sites after RA-induced differentiation were identified by ChIP-seq.
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| Web link |
https://oc-molgen.gnz.mpg.de/owncloud/s/H9a53oYiLFCmNPH
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| Contributor(s) |
Glaser LV, Fuchs A, Chung H, Meijsing SH |
| Citation(s) |
34850108 |
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https://doi.org/10.1093/nar/gkab1100
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| |
| Submission date |
Apr 09, 2021 |
| Last update date |
Dec 03, 2021 |
| Contact name |
Laura V Glaser |
| E-mail(s) |
glaser@molgen.mpg.de
|
| Phone |
+49 30 8413-1560
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| Organization name |
Max Planck Institute for Molecular Genetics
|
| Department |
Computational Molecular Biology
|
| Street address |
Ihnestraße 63-73
|
| City |
Berlin |
| ZIP/Postal code |
14195 |
| Country |
Germany |
| |
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| Platforms (2) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA720887 |
| SRA |
SRP314201 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE171771_FAIRE_STARR_LIFvsInp_RPGC_log2.bw |
50.0 Mb |
(ftp)(http) |
BW |
| GSE171771_FAIRE_STARR_LIFvsInp_RPGC_subtract.bw |
50.5 Mb |
(ftp)(http) |
BW |
| GSE171771_FAIRE_STARR_RAvsInp_RPGC_log2.bw |
49.7 Mb |
(ftp)(http) |
BW |
| GSE171771_FAIRE_STARR_RAvsInp_RPGC_subtract.bw |
50.2 Mb |
(ftp)(http) |
BW |
| GSE171771_FAIRE_STARR_enh_LIFdep.bed.gz |
18.0 Kb |
(ftp)(http) |
BED |
| GSE171771_FAIRE_STARR_enh_RAind.bed.gz |
11.6 Kb |
(ftp)(http) |
BED |
| GSE171771_FAIRE_STARR_enh_mESC.bed.gz |
140.7 Kb |
(ftp)(http) |
BED |
| GSE171771_FAIRE_STARR_enh_mESC_scored.tab.gz |
76.6 Kb |
(ftp)(http) |
TAB |
| GSE171771_RAW.tar |
503.6 Mb |
(http)(custom) |
TAR (of BED, BW, NARROWPEAK) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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