← BioTransfer GEO Dataset Finder
GEO series

Mosaic gastruloids reveal a temporal restriction for developmental cell competition

GSE294530 Mus musculus (mouse) RNA-seq (gene expression) 69 samples Submitted 2026/02/12 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 69 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
69 samples: 23 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
Mosaic gastruloids reveal a temporal restriction for developmental cell competitionNature cell biology · 2026
Summary (written by the submitters)
In early mammalian embryogenesis, the selective elimination of suboptimal cells is critical for developmental integrity. Cell competition is a non-autonomous quality control in which “winner” cells eliminate viable but suboptimal “loser” cells based on their relative difference in fitness. Due to its central role in fitness perception, loss of p53 results in the emergence of “supercompetitor” cells, which stand at the apex of cell competition and induce apoptosis in neighboring wild-type (WT) cells.
Read the full summary ↓
Here, we investigate cell competition dynamics using mosaic 3D mouse gastruloids, an embryonic stem cell (ESC)-based in vitro model of gastrulation, composed of defined numbers of WT and p53-KO cells. In mosaic gastruloids, even low numbers of p53-KO cells robustly outcompete WT cells, and introduction of as few as two p53-KO cells is sufficient to measurably impair neighboring WT cell growth. Cell competition in gastruloids is independent of proliferation rates, nutrient availability, or reactive oxygen species, and not influenced by Nodal and ERK signaling. However, we observe that Wnt and BMP signaling protect from cell competition, which is exclusively driven by intrinsic apoptosis, as indicated by Bcl2-mediated complete rescue of WT cells. During gastruloid development, cell competition is temporally restricted to a window of 48–96 hours after aggregation, mirroring embryonic days E5.5–E7.5 in the mouse. Heterochronic mosaic gastruloid experiments demonstrate that relative differences in pluripotency levels are neither necessary nor sufficient to cause supercompetition, but that cell competition is contingent on both competitors residing within the developmental window permissive to competition. Neither pluripotent mosaic 3D aggregates, nor 3D EpiGastruloids, which model more advanced developmental processes, display any competition, supporting the hypothesis that developmental cell competition is specific to the onset of gastrulation. Our findings offer insights into the mechanisms of cell fitness evaluation in mammalian embryogenesis and establish gastruloids as a powerful 3D model for investigating developmental stage-specific cell competition.
Published in
Mosaic gastruloids reveal a temporal restriction for developmental cell competition
Frenster JD, Babin S, Casani-Galdon P et al. · Nature cell biology 2026 · PMID 41922518 · doi:10.1038/s41556-026-01923-x
This dataset
Open GSE294530 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 GSE294530_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 PRJNA1250457 and SRA study SRP578434. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41922518) ↗
Study design
23 conditions, mostly in triplicate
WT-H2B-mCherry("F") mESC 0h ×3 WT-H2B-emiRFP670("W") mESC 0h ×3 p53KO-H2B-emiRFP670("K") mESC 0h ×3 Sorted WT-mCh (F) cells from WT+WT mosaic gas… ×3 Sorted WT-mCh (F) cells from WT+WT mosaic gas… ×3 Sorted WT-mCh (F) cells from WT+WT mosaic gas… ×3 Sorted WT-mCh (F) cells from WT+WT mosaic gas… ×3 Sorted WT-mCh (F) cells from WT+WT mosaic gas… ×3 +16 more

Supports a between-group comparison across 68 samples.

How we read this: 23 replicated groups read from 69 sample titles; they account for 68 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

+ 29 more — browse all 69 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.