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Comparative analysis of mouse strains for in vivo induction of reprogramming factors

GSE262157 Mus musculus (mouse) RNA-seq (gene expression) 96 samples Submitted 2025/05/04 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 96 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
96 samples: 32 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
Comparative analysis of mouse strains for in vivo induction of reprogramming factorsCell reports · 2025
Summary (written by the submitters)
In vivo reprogramming through the forced expression of Oct4, Sox2, Klf4, and c-Myc (OSKM) has demonstrated great potential for reversing age-associated phenotypes, as the combination of these transcription factors actively promote cell regeneration and rejuvenation in various tissues and organs. However, continuous in vivo OSKM expression raised safety concerns due to loss of cell identity, decrease in body weight, and premature death.
Read the full summary ↓
Although cyclic short-term or targeted expression of the reprogramming factors can mitigate some of these detrimental effects in mice, systemic rejuvenation of wild type mice has remained elusive potentially due to these current technical limitations. To improve the fundamental understanding of in vivo reprogramming, we conducted a comparative analysis across multiple reprogrammable mouse strains, tissues, and expression methods, presenting a comprehensive atlas of formerly established strains. In addition, we developed novel reprogrammable mouse strains by avoiding OSKM expression in specific organs, in dividing cells, or implementing chimeric expression approaches within specific cells, thereby offering safer strategies to induce in vivo reprogramming and fully harness its potential. We hope that these new tools will become valuable resources for future research in this very exciting field of research with potential implications to human health.
Published in
Comparative analysis of mouse strains for in vivo induction of reprogramming factors
Picó S, Vílchez-Acosta A, Agostinho de Sousa J et al. · Cell reports 2025 · PMID 40560729 · doi:10.1016/j.celrep.2025.115879
This dataset
Open GSE262157 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 GSE262157_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 PRJNA1090489 and SRA study SRP497033. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40560729) ↗
Study design
32 conditions, mostly in triplicate
Kidney control ×3 Kidney 4Fj ×3 Kidney 4FsB ×3 Kidney 4Fk ×3 Kidney 4FsA ×3 Liver control ×3 Liver 4Fj ×3 Liver 4FsB ×3 +25 more

Supports a between-group comparison across 95 samples.

How we read this: 32 replicated groups read from 96 sample titles; they account for 95 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

+ 56 more — browse all 96 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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