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KDM6A facilitates Xist upregulation at the onset of X inactivation [RNA-Seq]

GSE279278 Mus musculus (mouse) RNA-seq (gene expression) 18 samples Submitted 2025/01/08 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 18 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
18 samples: 9 conditions, mostly in duplicateGroups 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
KDM6A facilitates Xist upregulation at the onset of X inactivationBiology of sex differences · 2025
Summary (written by the submitters)
X chromosome inactivation (XCI) is a female-specific process in which one X chromosome is silenced to balance X-linked gene expression between the sexes. XCI is initiated in early development by upregulation of the lncRNA Xist on the future inactive X (Xi). A subset of X-linked genes escape silencing and thus have higher expression in females, suggesting female-specific functions.
Read the full summary ↓
One of these genes is the highly conserved gene Kdm6a, which encodes a histone demethylase that removes methyl groups at H3K27 to facilitate gene expression. Here, we investigate the role of KDM6A in the regulation of Xist. We observed impaired upregulation of Xist during early stages of differentiation in hybrid mouse ES cells following CRISPR/Cas9 knockout of Kdm6a. This is associated with reduced Xist RNA coating of the Xi, suggesting diminished XCI potency. Indeed, Kdm6a knockout results in aberrant overexpression of genes from the Xi after differentiation. KDM6A binds to the Xist promoter and knockout cells show an increase in H3K27me3 at Xist. These results indicate that KDM6A plays a role in the initiation of XCI through histone demethylase-dependent activation of Xist during early differentiation.
Published in
KDM6A facilitates Xist upregulation at the onset of X inactivation
Lin J, Zhang J, Ma L et al. · Biology of sex differences 2025 · PMID 39754175 · doi:10.1186/s13293-024-00683-3
This dataset
Open GSE279278 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 GSE279278_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 PRJNA1171795 and SRA study SRP537952. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39754175) ↗
Study design
9 conditions, mostly in duplicate
E8 stem cells, wildtype control, Day7, ×2 E8 stem cells, wildtype control, Day15, ×2 E8 stem cells, knockout, Day7, ×2 E8 stem cells, knockout, Day15, ×2 Tsix-stop cells, wildtype control, Day0, ×2 Tsix-stop cells, wildtype control, Day15, ×2 Tsix-stop cells, knockout, Day0, ×2 Tsix-stop cells, knockout, Day15, ×2 +1 more

Supports a case/control comparison: 8 samples read as cases, 10 as controls.

How we read this: 9 replicated groups read from 18 sample titles; they account for 18 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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