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The whole-genome duplication is a barrier for iPSCs reprogramming from mouse fibroblasts

GSE295779 Mus musculus (mouse) RNA-seq (gene expression) 28 samples Submitted 2026/05/15 Platform GPL21273
At a glance

RNA-seq (gene expression) · mouse · 28 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
28 samples: 14 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
Spontaneous whole genome duplication renders mouse embryonic fibroblasts resistant to reprogrammingCell & bioscience · 2026
Summary (written by the submitters)
Whole-genome duplication (WGD) -induced tetraploidization represents a pivotal genetic event widely investigated in the contexts of tumorigenesis, developmental processes, and evolutionary biology, whereas its functional consequences for somatic cell reprogramming have yet to be elucidated. Here we show that mouse embryonic fibroblasts (MEFs) undergo spontaneous WGD in vitro.
Read the full summary ↓
However, the resulting tetraploid cells are refractory to iPSCs reprogramming. Mechanistically, the tetraploidization of MEFs is p38-dependent. Pretreatment with p38 inhibitor SB203580 suppresses cytokinesis failure-induced binucleation and significantly enhances reprogramming efficiency. We further identify the elevated p53 accumulation in binucleated cells as the primary barrier to reprogramming, as its depletion rescues iPSCs formation in tetraploid cells. These findings reveal the whole-genome duplication exerts distinct regulatory control over cell fate transition.
Published in
Spontaneous whole genome duplication renders mouse embryonic fibroblasts resistant to reprogramming
Li W, Zhong L, Li P et al. · Cell & bioscience 2026 · PMID 41888895 · doi:10.1186/s13578-026-01558-3
This dataset
Open GSE295779 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 GSE295779_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 PRJNA1256352 and SRA study SRP581760. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41888895) ↗
Study design
14 conditions, mostly in duplicate
MEF.ctr ×2 MEF.p38i ×2 ctr.d1 ×2 ctr.d3 ×2 ctr.d5 ×2 ctr.d7 ×2 p38i.d1 ×2 p38i.d3 ×2 +6 more

Supports a between-group comparison across 28 samples.

How we read this: 14 replicated groups read from 28 sample titles; they account for 28 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
Datasets on a similar topic

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