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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 15, 2019 |
| Title |
Genome-wide profiling of transcription, H3K27me3 and RING1B occupancy in mouse ESCs following EZH1/2 inhibition |
| Organism |
Mus musculus |
| Experiment type |
Other
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Mouse embryonic stem cells (mESCs) were treated with DMSO (control) or EPZ-6438 (EPZ; a potent inhibitor of the EZH1/2) for 24 h. ChIP-seq was used to determine the impact of this treatment on the level and distribution of H3K27me3 and RING1B genome-wide. In parallel, gene expression was assessed by deep sequencing of both total RNA (RNA-seq) and 4-thiouridine metabolically labelled RNA (4sU-seq). Calibrated ChIP-seq, utilizing Drosophila chromatin as an exogenous control, demonstrated a marked global depletion of H3K27me3 following 24 h of EPZ treatment concomitant with a substantial reduction in RING1B occupancy. A rather modest change in the levels of total and nascent transcripts allowed us to identify a direct contribution of the polycomb system in controlling chromatin architecture and 3D nuclear organization.
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| Overall design |
Following 24 h of treatment with either DMSO or EPZ-6438, mESCs were processed for ChIP-seq (calibrated H3K27me3 and non-calibrated RING1B), RNA-seq and 4sU-seq. Two independent replicate experiments were prepared for each sample.
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| Contributor(s) |
Boyle S, Flyamer IM, Williamson I, Sengupta D, Bickmore WA, Illingworth RS |
| Citation(s) |
32439634 |
| Submission date |
Nov 23, 2019 |
| Last update date |
Jun 10, 2020 |
| Contact name |
Rob S Illingworth |
| E-mail(s) |
robert.illingworth@ed.ac.uk
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| Phone |
01316519640
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| Organization name |
The University of Edinburgh
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| Department |
Centre for regenerative Medicine
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| Lab |
Illingworth
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| Street address |
Centre for Regenerative Medicine
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| City |
Edinburgh |
| State/province |
Midlothian |
| ZIP/Postal code |
EH16 4UU |
| Country |
United Kingdom |
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| Platforms (1) |
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| Samples (20)
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| GSM4189766 |
mESCs, 4SU_EPZ_2 |
| GSM4189767 |
mESCs, totRNA_DMSO_1 |
| GSM4189768 |
mESCs, totRNA_DMSO_2 |
| GSM4189769 |
mESCs, totRNA_EPZ_1 |
| GSM4189770 |
mESCs, totRNA_EPZ_2 |
| GSM4189771 |
mESCs, Input_DMSO_1 |
| GSM4189772 |
mESCs, Input_DMSO_2 |
| GSM4189773 |
mESCs, Input_EPZ_1 |
| GSM4189774 |
mESCs, Input_EPZ_2 |
| GSM4189775 |
mESCs, K27me3_DMSO_1 |
| GSM4189776 |
mESCs, K27me3_DMSO_2 |
| GSM4189777 |
mESCs, K27me3_EPZ_1 |
| GSM4189778 |
mESCs, K27me3_EPZ_2 |
| GSM4189779 |
mESCs, RING1B_DMSO_1 |
| GSM4189780 |
mESCs, RING1B_DMSO_2 |
| GSM4189781 |
mESCs, RING1B_EPZ_1 |
| GSM4189782 |
mESCs, RING1B_EPZ_2 |
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| Relations |
| BioProject |
PRJNA591300 |
| SRA |
SRP231902 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE140894_RAW.tar |
6.4 Gb |
(http)(custom) |
TAR (of BIGWIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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