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| Status |
Public on Sep 30, 2019 |
| Title |
Genome-wide histone modification and accessibility maps of mESCs, in the pluripotent state and after induced differentiation |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
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 and chromatin accessibility. The identification of enhancers on a genome wide level is an important prerequisite for many functional studies, however the prediction of enhancer elements, especially with in response to changing conditions, remains challenging. Here we report the generation of a genome-wide mESC enhancer prediction map, comparing the pluripotent state and induced differentiation, by the integration of data on transcription, chromatin accessibility and multiple histone modifications.
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| Overall design |
mESCs, in the pluripotent state or after induced differentiation, were assessed for genome-wide changes in (i) gene expression by RNA-seq for poly-adenylated transcripts using biological triplicates, (ii) chromatin accessibility by ATAC-seq, and (iii) enrichment of eight specific chromatin marks by ChIP-seq.
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| Contributor(s) |
Glaser LV, Fuchs A, Chung H, Meijsing SH |
| Citation(s) |
31699133 |
| Submission date |
Sep 24, 2018 |
| Last update date |
Nov 18, 2019 |
| Contact name |
Laura V Glaser |
| E-mail(s) |
glaser@molgen.mpg.de
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| Phone |
+49 30 8413-1560
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| Organization name |
Max Planck Institute for Molecular Genetics
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| Department |
Computational Molecular Biology
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| 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) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (26)
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| Relations |
| BioProject |
PRJNA492903 |
| SRA |
SRP162460 |
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