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Aging promotes reactivation of the Barr body at distal chromosome regions [RNA organs]

GSE274689 Mus musculus (mouse) RNA-seq (gene expression) 141 samples Submitted 2025/03/21 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 141 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
141 samples: 47 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
Aging promotes reactivation of the Barr body at distal chromosome regionsNature aging · 2025
Summary (written by the submitters)
Decades ago, evidence of age-related reactivation of a single gene on the female inactive X chromosome was observed in mice. While stable silencing of the Barr body is crucial for balancing gene dosage between sexes, it remained unclear whether silencing is maintained during aging. Here, we employed allele-specific multi-omics approaches to capture a comprehensive catalog of genes escaping X chromosome inactivation throughout mouse development and aging.
Read the full summary ↓
We found substantially elevated escape rates during aging across organs, occurring in multiple distinct cell types and concentrated at distal chromosome regions. Consistently, chromatin accessibility was increased across multiple megabases at chromosome ends, affecting regulatory elements of escapees. Since several age-specific escapees are linked to human diseases, their elevated expression in females might contribute to sex-biased disease progression observed during aging.
Published in
Aging promotes reactivation of the Barr body at distal chromosome regions
Hoelzl S, Hasenbein TP, Engelhardt S et al. · Nature aging 2025 · PMID 40312568 · doi:10.1038/s43587-025-00856-8
This dataset
Open GSE274689 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 GSE274689_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 PRJNA1147659 and SRA study SRP526370. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40312568) ↗
Study design
47 conditions, mostly in triplicate
Br_E14.5_RNA_XistBxC_-+_XX ×3 Br_4w_RNA_XistBxC_-+_XX ×3 Br_4w_RNA_XistBxC_+y_XY ×3 Br_9w_RNA_XistBxC_-+_XX ×3 Br_9w_RNA_XistBxC_+y_XY ×3 Br_78w_RNA_XistBxC_-+_XX ×3 Br_78w_RNA_XistBxC_+y_XY ×3 He_E14.5_RNA_XistBxC_-+_XX ×3 +39 more

Supports a between-group comparison across 141 samples.

How we read this: 47 replicated groups read from 141 sample titles; they account for 141 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

+ 101 more — browse all 141 samples with per-sample file links →

Datasets on a similar topic

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