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Trans-regulation of heterochromatin underlies genetic variation in 3D genome contacts

GSE312918 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 69 samples Submitted 2026/01/30 Platform GPL19057Platform GPL34290
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 69 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
69 samples: 20 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
Trans-regulation of heterochromatin underlies genetic variation in 3D genome contactsbioRxiv : the preprint server for 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
Trans-regulation of heterochromatin underlies genetic variation in 3D genome contacts
Fortin HJ, Struba AZ, Baker CL · bioRxiv : the preprint server for biology 2025 · PMID 41427289 · doi:10.64898/2025.12.10.693515
This dataset
Open GSE312918 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 GSE312918_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 PRJNA1377595 and SRA study SRP681754. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41427289) ↗
Study design
20 conditions, mostly in triplicate
B6 5-1, mouse embryonic stem cells, technical ×3 D2 5-5, mouse embryonic stem cells, technical ×3 XE 2-4, mouse embryonic stem cells, technical ×3 B6 5-1, mouse embryonic stem cells, H3K9me3 (… ×3 XE 2-4, mouse embryonic stem cells, H3K9me3 (… ×3 B6 5-1, mouse embryonic stem cells, H3K27ac (… ×3 D2 5-5, mouse embryonic stem cells, H3K27ac (… ×3 QJ 6-1, mouse embryonic stem cells, H3K27ac (… ×3 +29 more

Supports a between-group comparison across 52 samples.

How we read this: 20 replicated groups read from 69 sample titles; they account for 52 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

+ 29 more — browse all 69 samples with per-sample file links →

Datasets on a similar topic

Search all mouse ChIP / ATAC / CUT&Tag datasets in GEO →

Share this dataset

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