GEO series
Dual Role of PRC2-EZH1 in Orchestrating Rhythmicity of Circadian Transcriptional Program in Post-mitotic Skeletal Muscle Cells
GSE198409
Mus musculus (mouse)
ChIP-seq / ATAC-seq (genome binding and open chromatin)
78 samples
Submitted 2025/01/03
Platform GPL24247
At a glance
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 78 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Mus musculus (mouse)
- Samples
- 78 samples: 24 conditions, mostly in triplicateGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- PRC2-EZH1 contributes to circadian gene expression by orchestrating chromatin states and RNA polymerase II complex stabilityThe EMBO journal · 2024
Summary (written by the submitters)
Circadian rhythmicity of gene expression is a conserved feature of cell physiology. This involves the fine tuning between transcriptional and post-transcriptional molecular mechanisms, strongly dependent on the metabolic state of the cell that guarantees intrinsic plasticity of tissue specific genetic programs. To support the plastic properties a key role is played by the dynamics of epigenome structure and its regulators.
Read the full summary ↓
Here we investigate the role of the Polycomb cell memory complex PRC2-EZH1 in regulating transcriptional rhythmicity in post-mitotic skeletal muscle cells. We show that PRC2-EZH1 core components are under direct regulation of BMAL1, show an oscillatory behavior and control both silencing and activation of target genes. Fully assembled PRC2-EZH1 complex negatively regulates cyclic expression of direct targets through modulation of cyclic H3K27me3 status. Conversely, we show that EZH1 regulates constitutive circadian genes expression, through stabilization of RNA Pol II machinery and maintenance of transcription process fidelity. Collectively, these findings unveil the dual and multi role of PcG in circadian gene regulation in adult skeletal muscle cells, and the plastic nature of PcG cell memory system in somatic cells.
Published in
Liu P, Nadeef S, Serag MF et al.
· The EMBO journal 2024
· PMID 39433902
· doi:10.1038/s44318-024-00267-2
This dataset
Download · which file do I need?
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
1 · Just have a look
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
2 · Re-analyse it
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE198409_RAW.tar (it can run to tens of gigabytes).
3 · Start from the raw reads
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA774105 and SRA study SRP342938. Searching any of these in the dataset finder brings you back here.
Study design
24 conditions, mostly in triplicate
Bio-EZH1 ChIP-seq at 12h, ×3
Bio-EZH1 ChIP-seq at 16h, ×3
Bio-EZH1 ChIP-seq at 20h, ×3
Bio-EZH1 ChIP-seq at 24h, ×3
Bio-EZH1 ChIP-seq at 28h, ×3
Bio-EZH1 ChIP-seq at 32h, ×3
SUZ12 ChIP-seq at 12h, ×3
SUZ12 ChIP-seq at 16h, ×3
+24 more
Supports a between-group comparison across 70 samples.
How we read this: 24 replicated groups read from 78 sample titles; they account for 70 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
Samples in this study
- GSM7899978 Bio-EZH1 ChIP-seq at 12h, biological replicate 1 Bio-EZH1 ChIP-seq at 12…
- GSM7899979 Bio-EZH1 ChIP-seq at 12h, biological replicate 2 Bio-EZH1 ChIP-seq at 12…
- GSM7899980 Bio-EZH1 ChIP-seq at 12h, biological replicate 3 Bio-EZH1 ChIP-seq at 12…
- GSM7899981 Bio-EZH1 ChIP-seq at 16h, biological replicate 1 Bio-EZH1 ChIP-seq at 16…
- GSM7899982 Bio-EZH1 ChIP-seq at 16h, biological replicate 2 Bio-EZH1 ChIP-seq at 16…
- GSM7899983 Bio-EZH1 ChIP-seq at 16h, biological replicate 3 Bio-EZH1 ChIP-seq at 16…
- GSM7899984 Bio-EZH1 ChIP-seq at 20h, biological replicate 1 Bio-EZH1 ChIP-seq at 20…
- GSM7899985 Bio-EZH1 ChIP-seq at 20h, biological replicate 2 Bio-EZH1 ChIP-seq at 20…
- GSM7899986 Bio-EZH1 ChIP-seq at 20h, biological replicate 3 Bio-EZH1 ChIP-seq at 20…
- GSM7899987 Bio-EZH1 ChIP-seq at 24h, biological replicate 1 Bio-EZH1 ChIP-seq at 24…
- GSM7899988 Bio-EZH1 ChIP-seq at 24h, biological replicate 2 Bio-EZH1 ChIP-seq at 24…
- GSM7899989 Bio-EZH1 ChIP-seq at 24h, biological replicate 3 Bio-EZH1 ChIP-seq at 24…
- GSM7899990 Bio-EZH1 ChIP-seq at 28h, biological replicate 1 Bio-EZH1 ChIP-seq at 28…
- GSM7899991 Bio-EZH1 ChIP-seq at 28h, biological replicate 2 Bio-EZH1 ChIP-seq at 28…
- GSM7899992 Bio-EZH1 ChIP-seq at 28h, biological replicate 3 Bio-EZH1 ChIP-seq at 28…
- GSM7899993 Bio-EZH1 ChIP-seq at 32h, biological replicate 1 Bio-EZH1 ChIP-seq at 32…
- GSM7899994 Bio-EZH1 ChIP-seq at 32h, biological replicate 2 Bio-EZH1 ChIP-seq at 32…
- GSM7899995 Bio-EZH1 ChIP-seq at 32h, biological replicate 3 Bio-EZH1 ChIP-seq at 32…
- GSM7899996 SUZ12 ChIP-seq at 12h, biological replicate 1 SUZ12 ChIP-seq at 12h,
- GSM7899997 SUZ12 ChIP-seq at 12h, biological replicate 2 SUZ12 ChIP-seq at 12h,
- GSM7899998 SUZ12 ChIP-seq at 12h, biological replicate 3 SUZ12 ChIP-seq at 12h,
- GSM7899999 SUZ12 ChIP-seq at 16h, biological replicate 1 SUZ12 ChIP-seq at 16h,
- GSM7900000 SUZ12 ChIP-seq at 16h, biological replicate 2 SUZ12 ChIP-seq at 16h,
- GSM7900001 SUZ12 ChIP-seq at 16h, biological replicate 3 SUZ12 ChIP-seq at 16h,
- GSM7900002 SUZ12 ChIP-seq at 20h, biological replicate 1 SUZ12 ChIP-seq at 20h,
- GSM7900003 SUZ12 ChIP-seq at 20h, biological replicate 2 SUZ12 ChIP-seq at 20h,
- GSM7900004 SUZ12 ChIP-seq at 20h, biological replicate 3 SUZ12 ChIP-seq at 20h,
- GSM7900005 SUZ12 ChIP-seq at 24h, biological replicate 1 SUZ12 ChIP-seq at 24h,
- GSM7900006 SUZ12 ChIP-seq at 24h, biological replicate 2 SUZ12 ChIP-seq at 24h,
- GSM7900007 SUZ12 ChIP-seq at 24h, biological replicate 3 SUZ12 ChIP-seq at 24h,
- GSM7900008 SUZ12 ChIP-seq at 28h, biological replicate 1 SUZ12 ChIP-seq at 28h,
- GSM7900009 SUZ12 ChIP-seq at 28h, biological replicate 2 SUZ12 ChIP-seq at 28h,
- GSM7900010 SUZ12 ChIP-seq at 28h, biological replicate 3 SUZ12 ChIP-seq at 28h,
- GSM7900011 SUZ12 ChIP-seq at 32h, biological replicate 1 SUZ12 ChIP-seq at 32h,
- GSM7900012 SUZ12 ChIP-seq at 32h, biological replicate 2 SUZ12 ChIP-seq at 32h,
- GSM7900013 SUZ12 ChIP-seq at 32h, biological replicate 3 SUZ12 ChIP-seq at 32h,
- GSM7900014 H3K27me3 ChIP-seq at 12h, biological replicate 1 H3K27me3 ChIP-seq at 12…
- GSM7900015 H3K27me3 ChIP-seq at 12h, biological replicate 2 H3K27me3 ChIP-seq at 12…
- GSM7900016 H3K27me3ChIP-seq at 12h, biological replicate 3
- GSM7900017 H3K27me3 ChIP-seq at 16h, biological replicate 1 H3K27me3 ChIP-seq at 16…
+ 38 more — browse all 78 samples with per-sample file links →
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Share this dataset
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.