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B cell stimulation changes the structure and higher-order organization of the inactive X chromosome

GSE283966 Mus musculus (mouse) RNA-seq (gene expression) 15 samples Submitted 2024/12/31 Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 15 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
15 samples: 4 × Naïve CD23+ Follicular B Cells, Xist cKO, vs 4 × 24hr CpG Stimulated CD23+ Follicular B Cells, WT, vs 4 × 24hr CpG Stimulated CD23+ Follicular B Cells, Xist cKO, vs 3 × Naïve CD23+ Follicular B Cells, WT,Groups 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
B cell stimulation changes the structure and higher-order organization of the inactive X chromosomeCell reports · 2025
Summary (written by the submitters)
X Chromosome Inactivation (XCI) equalizes X-linked gene expression between sexes. B cells exhibit dynamic XCI, with Xist RNA/heterochromatic marks absent on the inactive X (Xi) in naive B cells but returning following mitogenic stimulation. The impact of dynamic XCI on Xi structure and maintenance was previously unknown. Here, we find dosage compensation of the Xi with state-specific XCI escape genes in naive and in vitro activated B cells.
Read the full summary ↓
Allele-specific OligoPaints indicate similar Xi and Xa territories in B cells that are less compact than in fibroblasts. Allele-specific Hi-C reveals a lack of TAD-like structures on the Xi of naive B cells, and stimulation-induced alterations in TAD-like boundary strength independent of gene expression. Notably, Xist deletion in B cells changes TAD boundaries and large-scale Xi compaction. Altogether, our results uncover B cell-specific Xi plasticity which could underlie sex-biased biological mechanisms.
Published in
B cell stimulation changes the structure and higher-order organization of the inactive X chromosome
Sierra I, Toothacre NE, van der Weide RH et al. · Cell reports 2025 · PMID 40014450 · doi:10.1016/j.celrep.2025.115351
This dataset
Open GSE283966 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 GSE283966_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1196421 and SRA study SRP550570. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40014450) ↗
Study design
4 × Naïve CD23+ Follicular B Cells, Xist cKO, vs 4 × 24hr CpG Stimulated CD23+ Follicular B Cells, WT, vs 4 × 24hr CpG Stimulated CD23+ Follicular B Cells, Xist cKO, vs 3 × Naïve CD23+ Follicular B Cells, WT,

Supports a case/control comparison: 4 samples read as cases, 3 as controls.

How we read this: 4 replicated groups read from 15 sample titles; they account for 15 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
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