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Transcription-dependent heterochromatin at the Xist promoter shapes the random choice of the inactive X chromosome

GSE339369 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 245 samples Submitted 2026/07/25 Platform GPL16417Platform GPL30172Platform GPL28457Platform GPL24247Platform GPL34475
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 245 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
245 samples: 64 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.
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
This dataset
Open GSE339369 in finder → Find more mouse methylation 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 GSE339369_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 PRJNA1498523 and SRA study SRP718842. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
64 conditions, mostly in triplicate
F121.9 WT Day4 ×7 F121.9 RNF12-KO Day4 ×7 CasTuner sgRnf12 KD Day3 ×6 CasTuner sgRnf12 ctrl Day3 ×6 CasTuner sgZic3 KD Day3 ×6 CasTuner sgZic3 ctrl Day3 ×6 CasTuner sgZfp280c KD Day4 ×6 CasTuner sgZfp280c ctrl Day4 ×6 +56 more

Supports a case/control comparison: 12 samples read as cases, 82 as controls.

How we read this: 64 replicated groups read from 245 sample titles; they account for 245 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

+ 205 more — browse all 245 samples with per-sample file links →

Datasets on a similar topic

Search all mouse methylation datasets in GEO →

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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.