← BioTransfer GEO Dataset Finder
GEO series

OTX2 controls chromatin accessibility to direct somatic versus germline differentiation [ATAC-Seq]

GSE289298 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 32 samples Submitted 2025/02/17 Platform GPL30172Platform GPL24247Platform GPL21626
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 32 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
32 samples: 16 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
OTX2 controls chromatin accessibility to direct somatic versus germline differentiationEMBO reports · 2026
Summary (written by the submitters)
The choice between somatic and germline fates is essential for species survival. This choice occurs in embryonic epiblast cells, as these cells are competent for both somatic and germline differentiation. Transcription factors (TFs) play a central role in this process by binding to specific chromatin loci to modulate gene expression and determine cell identity.
Read the full summary ↓
The TF OTX2 regulates the choice between somatic and germline fates, as Otx2-null epiblast-like cells (EpiLCs) form primordial germ cell-like cells (PGCLCs) with enhanced efficiency. However, the mechanisms by which OTX2 achieves this function are not fully characterized. Here we show that OTX2 controls chromatin accessibility to enable somatic differentiation. By performing CUT&RUN for OTX2 and ATAC-seq in wild-type and Otx2-null embryonic stem cells and EpiLCs, we identified regions where OTX2 binding opens chromatin. Enforced OTX2 expression maintains accessibility at these regions and induces opening of 4,000 additional somatic-associated regions in the presence of PGC-inducing cytokines. Once cells have acquired germline identity, the 4,000 additional somatic associated regions do not respond to OTX2 and remain closed. Our results indicate that OTX2 works in cells with dual competence for both somatic and germline differentiation to increase accessibility of somatic regulatory regions and induce the somatic fate at the expense of the germline.
Published in
OTX2 controls chromatin accessibility to direct somatic versus germline differentiation
Barbieri E, Chambers I · EMBO reports 2026 · PMID 41361697 · doi:10.1038/s44319-025-00622-2
This dataset
Open GSE289298 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 GSE289298_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 PRJNA1222363 and SRA study SRP563214. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41361697) ↗
Study design
16 conditions, mostly in duplicate
ATAC-seq WT ESCs ×2 ATAC-seq WT EpiLCs ×2 ATAC-seq WT PGCLC aggregates, no cytokines, d… ×2 ATAC-seq Otx2-/- 2i/LIF ESCs ×2 ATAC-seq Otx2-/- EpiLCs ×2 ATAC-seq Otx2-/- PGCLC aggregates, plus cytok… ×2 ATAC-seq Otx2-/- OTX2-ERT2 EpiLCs, untreated, ×2 ATAC-seq Otx2-/- OTX2-ERT2 EpiLCs, Tamoxifen … ×2 +8 more

Supports a between-group comparison across 32 samples.

How we read this: 16 replicated groups read from 32 sample titles; they account for 32 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

Search all mouse ChIP / ATAC / CUT&Tag 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.