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Totipotent-Like Cell-Based Embryo Model Recapitulating Mouse Embryogenesis from Pre-Implantation to Gastrulation [RNA-Seq]

GSE287908 Mus musculus (mouse) RNA-seq (gene expression) 52 samples Submitted 2025/09/18 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 52 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
52 samples: 26 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
A continuous totipotent-like cell-based embryo model recapitulates mouse embryogenesis from zygotic genome activation to gastrulationNature cell biology · 2025
Summary (written by the submitters)
The development of stem-cell-derived models of mammalian embryogenesis has provided invaluable tools for investigating embryo development. However, constructing embryo models that can continuously recapitulate the full developmental trajectory, from zygotic genome activation (ZGA) to gastrulation, remains a major challenge. Here, we developed a new chemical cocktail to induce totipotent-like cells with robust proliferation ability, and leveraged these cells to establish a stepwise protocol to generate a continuous embryo model.
Read the full summary ↓
This model sequentially mimics mouse embryogenesis from embryonic day 1.5 to 7.5. It recapitulates key developmental milestones, including ZGA in 2-cell embryos, the diversification of embryonic and extraembryonic lineages from 4-cell to 64-cell stages, the formation of blastocysts, and the subsequent development into post-implantation egg cylinders. Notably, these structures can undergo gastrulation, as evidenced by primitive streak formation and the subsequent emergence of several hallmarks of early organogenesis. Our study opens new avenues for modeling mammalian embryogenesis in vitro.
Published in
A continuous totipotent-like cell-based embryo model recapitulates mouse embryogenesis from zygotic genome activation to gastrulation
Ren Y, Wang X, Liu H et al. · Nature cell biology 2025 · PMID 41094030 · doi:10.1038/s41556-025-01793-9
This dataset
Open GSE287908 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 GSE287908_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 PRJNA1215263 and SRA study SRP559643. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41094030) ↗
Study design
26 conditions, mostly in duplicate
mouse extended totipotent stem cell ×2 mouse extended pluripotent stem cell EPS +CHI… ×2 mouse extended pluripotent stem cell EPS +CHI… ×2 mouse extended pluripotent stem cell EPS +CHI… ×2 mouse extended pluripotent stem cell EPS +CHI… ×2 mouse extended pluripotent stem cell EPS ×2 mESC ×2 mESC-S1 ×2 +18 more

Supports a between-group comparison across 52 samples.

How we read this: 26 replicated groups read from 52 sample titles; they account for 52 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

+ 12 more — browse all 52 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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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.