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DNA methylation shapes the Polycomb landscape during the exit from naive pluripotency

GSE242201 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 39 samples Submitted 2024/07/16 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 39 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
39 samples: 17 conditions, mostly in duplicateGroups 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
DNA methylation shapes the Polycomb landscape during the exit from naive pluripotencyNature structural & molecular biology · 2025
Summary (written by the submitters)
To formally assess how 5mC shapes the H3K27me3 landscape, we profiled the epigenome of naive and differentiated cells in the presence and absence of the DNA methylation machinery.
Published in
DNA methylation shapes the Polycomb landscape during the exit from naive pluripotency
Richard Albert J, Urli T, Monteagudo-Sánchez A et al. · Nature structural & molecular biology 2025 · PMID 39448850 · doi:10.1038/s41594-024-01405-4
This dataset
Open GSE242201 in finder → Find more mouse ChIP / ATAC / CUT&Tag datasets →
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.

Series matrix ↓
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 GSE242201_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
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.

Raw reads on ENA ↗

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 PRJNA1011970 and SRA study SRP458075. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39448850) ↗
Study design
17 conditions, mostly in duplicate
D7_DnmtWT_H3K36me3 ×3 D7_DnmtTKO_H3K36me3 ×3 D0_DnmtWT_H3K27me3 ×2 D0_DnmtTKO_H3K27me3 ×2 D7_DnmtWT_H3K27me3 ×2 D7_DnmtTKO_H3K27me3 ×2 D7_DnmtTKO_EzhipKO_H3K27me3 ×2 D0_DnmtWT_H3K36me3 ×2 +12 more

Supports a between-group comparison across 36 samples.

How we read this: 17 replicated groups read from 39 sample titles; they account for 36 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
Datasets on a similar topic

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