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SETDB1/HUSH modulates Xist RNA levels during establishment of X chromosome inactivation

GSE309424 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 292 samples Submitted 2026/03/12 Platform GPL19057
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 292 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
292 samples: 211 distinct titles, 27 of them repeatedGroups 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
SETDB1 and HUSH modulate Xist RNA levels during establishment of X chromosome inactivationNature communications · 2026
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
SETDB1 and HUSH modulate Xist RNA levels during establishment of X chromosome inactivation
Almeida M, Wei G, Cawte AD et al. · Nature communications 2026 · PMID 41957023 · doi:10.1038/s41467-026-71569-8
This dataset
Open GSE309424 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 GSE309424_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 PRJNA1336058 and SRA study SRP629422. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41957023) ↗
Study design
211 distinct titles, 27 of them repeated
FKBP-SETDB1 A12A10, Control, NPC d ×9 FKBP-SETDB1 G6D2, Control, NPC d ×9 FKBP-SETDB1 P2F7, Control, NPC d ×9 FKBP-SETDB1 A12A10, dTAGd1, NPC d ×8 FKBP-SETDB1 G6D2, dTAGd1, NPC d ×8 TsixStop NPCd ×8 FKBP-SETDB1 P2F7, dTAGd1, NPC d ×8 FKBP-SETDB1 A12A10, Control, Input, NPCd ×3 +19 more

How we read this: Read from 292 sample titles: 211 distinct titles with little repetition. 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

+ 252 more — browse all 292 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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