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Recruitment to the nuclear periphery enhances repression of H3K9me2-marked genes and transposons to shape cell fate

GSE288128 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 145 samples Submitted 2025/01/27 Platform GPL30172Platform GPL24247Platform GPL34290
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 145 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
145 samples: 37 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
The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fateNature cell biology · 2025
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fate
Marin HC, Allen C, Simental E et al. · Nature cell biology 2025 · PMID 40696106 · doi:10.1038/s41556-025-01703-z
This dataset
Open GSE288128 in finder → Find more mouse RNA-seq 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 GSE288128_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 PRJNA1216234 and SRA study SRP503412. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40696106) ↗
Study design
37 conditions, mostly in triplicate
mESC, naive pluripotency, WT, ×12 EpiLC, primed pluripotency, WT, ×8 mESC, naive pluripotency, TKO, ×8 mESC, naive pluripotency, QKO, ×8 mESC, naive pluripotency, LBRKO, ×4 EpiLC, primed pluripotency, LBRKO, ×4 EpiLC, primed pluripotency, TKO, ×4 EpiLC, primed pluripotency, QKO, ×4 +29 more

Supports a between-group comparison across 145 samples.

How we read this: 37 replicated groups read from 145 sample titles; they account for 145 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

+ 105 more — browse all 145 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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.