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Xist RNA Dependent and Independent Mechanisms Regulate Dynamic X Chromosome Inactivation in B Lymphocytes [CUTandRUN_F1]

GSE282253 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 64 samples Submitted 2026/03/17 Platform GPL30172Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 64 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
64 samples: 18 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
Xist RNA dependent and independent mechanisms regulate dynamic X chromosome inactivation in B lymphocytesCell reports · 2026
Summary (written by the submitters)
X-chromosome inactivation (XCI) maintenance in female B cells is dynamic (dXCI), where naïve cells lack cytological enrichment of Xist RNA and heterochromatic marks on the inactive X-chromosome (Xi), and these marks re-localize after stimulation. Here, we report the epigenetic profiling of silencing (H3K27me3, H2AK119Ub, H3K9me3, DNA methylation (DNAm)) and activating (H3K27ac) marks on the Xi during dXCI and investigate the requirement for Xist RNA in maintaining the Xi epigenetic landscape.
Read the full summary ↓
We find that the Xi in naïve B cells is depleted for H2AK119Ub and H3K9me3 but enriched for DNAm and H3K27me3 which maintain an epigenetic memory of transcriptional silencing dependent on Xist RNA. Upon stimulation, Xist-independent H3K27me3 and Xist-dependent H2AK119Ub modifications accumulate across the Xi. Thus, naïve B cells maintain an epigenetic memory of silencing in the absence of Xist RNA localization via retention of DNAm and H3K27me3, and both H3K27me3 and H2AK119Ub accumulate on the Xi post-stimulation in an Xist-dependent and -independent manner. These data have critical implications for understanding molecular mechanisms underlying female-biased immune responses.
Published in
Xist RNA dependent and independent mechanisms regulate dynamic X chromosome inactivation in B lymphocytes
Toothacre NE, Rodríguez-Acevedo KL, Wiggins KJ et al. · Cell reports 2026 · PMID 41964951 · doi:10.1016/j.celrep.2026.117254
This dataset
Open GSE282253 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 GSE282253_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 PRJNA1187779 and SRA study SRP546060. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41964951) ↗
Study design
18 conditions, mostly in triplicate
Spleen, CD23+ B cell, F1, 24h stimulated, H2A… ×5 Spleen, CD23+ B cell, F1, 24h stimulated, H3K… ×4 Spleen, CD23+ B cell, F1, 0h naïve, H2AK119Ub… ×4 Spleen, CD23+ B cell, F1, 0h naïve, H3K29me3,… ×4 Spleen, CD23+ B cell, F1, 12h stimulated, H3K… ×4 Spleen, CD23+ B cell, F1, 24h stimulated, H3K… ×4 Spleen, CD23+ B cell, F1, 0h naïve, H3K27me3,… ×3 Spleen, CD23+ B cell, F1, 12h stimulated, H3K… ×3 +13 more

Supports a between-group comparison across 61 samples.

How we read this: 18 replicated groups read from 64 sample titles; they account for 61 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

+ 24 more — browse all 64 samples with per-sample file links →

Datasets on a similar topic

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