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Mapping early PRC2 nucleation sites upon Suz12 reintroduction reveals features of de novo Polycomb recruitment

GSE305054 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 18 samples Submitted 2026/02/25 Platform GPL19057Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 18 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
18 samples: 9 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
Mapping early PRC2 nucleation sites upon Suz12 reintroduction reveals features of de novo Polycomb recruitmentbioRxiv : the preprint server for biology · 2025
Summary (written by the submitters)
Polycomb domains safeguard cell identity by maintaining lineage-specific chromatin states enriched in repressive histone modifications preserving the epigenetic memory of each cell lineage. While Polycomb Repressive Complex 2 (PRC2) can re-establish its occupancy after perturbation, the mechanisms that guide de novo Poly-comb recruitment remain unclear.
Read the full summary ↓
To address this, we engineered an auxin-inducible degradation system to reversibly deplete and reintroduce the endogenous PRC2 core subunit Suz12 in mouse embryonic stem cells (mESCs). Genome-wide profiling at early recovery time point revealed PRC2 nucleation sites, characterized by rapid Suz12 and H3K27me3 re-accumulation and signal strength.
Published in
Mapping early PRC2 nucleation sites upon Suz12 reintroduction reveals features of de novo Polycomb recruitment
Hernández-Romero IA, Peralta-Alvarez CA, Román-Figueroa A et al. · bioRxiv : the preprint server for biology 2025 · PMID 40950132 · doi:10.1101/2025.09.02.673664
This dataset
Open GSE305054 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 GSE305054_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 PRJNA1304372 and SRA study SRP608021. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40950132) ↗
Study design
9 conditions, mostly in duplicate
mESC, Suz12-mAID-mClover, Auxin ×2 mESC, H3K27me3, Auxin ×2 mESC, Suz12-mAID-mClover, Control ×2 mESC, H3K27me3, Control ×2 mESC, Suz12-mAID-mClover, Re-introduction ×2 mESC, H3K27me3, Re-introduction ×2 mESC, H2AK119ub1, Auxin ×2 mESC, H2AK119ub1, Control ×2 +1 more

Supports a between-group comparison across 18 samples.

How we read this: 9 replicated groups read from 18 sample titles; they account for 18 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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