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The impact of TRF2 deletion on gene expression profile of muscle stem cells

GSE263262 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2026/08/06 Platform GPL32159
At a glance

RNA-seq (gene expression) · mouse · 16 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
16 samples: 4 × Primary muscle stem cells, Wild type uninjured, vs 4 × Primary muscle stem cells, TRF2 knockout uninjured, vs 4 × Primary muscle stem cells, Wild type 3 days post-injury, vs 4 × Primary muscle stem cells, TRF2 knockout 3 days post-injury,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
TRF2 couples muscle stem cell identity to regenerative repairScience advances · 2026
Summary (written by the submitters)
Telomeric proteins are present in all mammalian cells protecting chromosomal ends and ensuring organismal homeostasis. However, it was also suggested that they have additional roles in certain tissues. Muscle stem cells (MuSCs), expressing a pivotal transcription factor Pax7, are fundamental to preserve regenerative capacity of muscle tissue.
Read the full summary ↓
Yet, the cell autonomous mechanism that regulates Pax7 expression to maintain MuSC identity is unclear. Here, we uncover that the telomeric protein TRF2 is critical to sustain stem cell identity in adult muscles and is dynamically regulated upon injury. MuSC-specific TRF2 ablation in mice aggravates muscular dystrophy, mimicking closely the severity of the human disease. Mechanistically, TRF2 directly binds to the regulatory regions of Pax7 gene and affects its expression. These findings identify a unique non-telomeric TRF2 function essential for transcribing Pax7 gene, a master stem cell regulator of the myogenic lineage, to modulate cellular properties indispensable for stem cell maintenance.
Published in
TRF2 couples muscle stem cell identity to regenerative repair
Lee JH, Nakka KK, Calhoun RP et al. · Science advances 2026 · PMID 42536731 · doi:10.1126/sciadv.aei7316
This dataset
Open GSE263262 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 GSE263262_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 PRJNA1096362 and SRA study SRP499836. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42536731) ↗
Study design
4 × Primary muscle stem cells, Wild type uninjured, vs 4 × Primary muscle stem cells, TRF2 knockout uninjured, vs 4 × Primary muscle stem cells, Wild type 3 days post-injury, vs 4 × Primary muscle stem cells, TRF2 knockout 3 days post-injury,

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

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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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