GEO series

SETDB1/HUSH modulates Xist RNA levels during establishment of X chromosome inactivation [ChIP-Seq, 2]

GSE312320 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 132 samples Submitted 2026/03/12 Platform GPL19057

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 132 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: 132 samples
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

Summary (written by the submitters)

The non-coding RNA Xist mediates X chromosome inactivation (XCI) in mammals, functioning in cis to direct heterochromatin formation over a single X chromosome in cells of early female embryos. Prior studies have determined that Xist transcription and turnover are modulated to maintain the correct level of Xist RNA to inactivate a single X chromosome.

Read the full summary ↓

The underlying molecular mechanisms are poorly understood. In this study we demonstrate that RNA-dependent recruitment of the H3K9me3 methyltransferase SETDB1 and the HUSH complex across the transcribed Xist locus functions to suppress Xist transcription during establishment of XCI. Thus, degron-mediated acute depletion of SETDB1 or core HUSH subunits abrogates allelic H3K9me3 deposition, increasing Xist transcription, accumulation of Xist RNA, and the rate of X chromosome gene silencing. Our findings support a model in which the SETDB1/HUSH pathway coordinates Xist transcription rates to maintain optimal Xist RNA levels, ensuring the silencing of a single X chromosome.

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 GSE312320 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 GSE312320_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 PRJNA1373024 and SRA study SRP650984. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41957023) ↗

Samples in this study

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+ 132 more — browse all 132 samples with per-sample file links →

Datasets on a similar topic

GSE309423 SETDB1/HUSH modulates Xist RNA levels during establishment of X chromosome inactivation [ChIP-Seq] 42 samples shares setdb1, hush, establishment, inactivation, chromosome, modulates, chip-seq, levels
GSE309424 SETDB1/HUSH modulates Xist RNA levels during establishment of X chromosome inactivation 292 samples shares setdb1, hush, establishment, inactivation, chromosome, modulates, levels
GSE310108 SETDB1/HUSH modulates Xist RNA levels during establishment of X chromosome inactivation [RNA-Seq] 112 samples shares setdb1, hush, establishment, inactivation, chromosome, modulates, levels
GSE206180 Stepwise de novo establishment of inactive X chromosome architecture in early development [XEN cells ChIP-seq] 20 samples shares establishment, chromosome, chip-seq
GSE247618 Histone methyltransferase SETDB1 silenced SINE B2 retrotransposons and maintained mitotic cell cycle of neural progenitor cells (ChIP-Seq) 12 samples shares setdb1, chip-seq
GSE303384 Mechanism of maintenance and establishment of repression by the Mtg16 tumor suppressor [CUT&RUN, ChIP-Seq] 92 samples shares establishment, chip-seq
GSE282254 Xist RNA Dependent and Independent Mechanisms Regulate Dynamic X Chromosome Inactivation in B Lymphocytes [CUTandRUN_Xist] 77 samples shares inactivation, chromosome
GSE329244 Polycomb erasers BAP1 and UTX are dispensable for rapid bivalent gene activation but essential for enhancer establishment [ChIP-seq] 64 samples shares establishment, chip-seq

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