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Trophectoderm-like cells from EPS cells enable generating EPS cell-derived post-implantation embryoids that complete gastrulation [bulk RNA-seq]

GSE291068 Mus musculus (mouse) Single-cell RNA-seq 34 samples Submitted 2025/10/21 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 34 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
34 samples: 16 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
Trophectoderm-like cells from EPS cells enable generating EPS cell-derived post-implantation embryoids that complete gastrulationProtein & cell · 2026
Summary (written by the submitters)
Mouse extended pluripotent stem (EPS) cells have demonstrated significant potential for generating embryo models in vitro. However, their limited capacity for extraembryonic trophoblast development has hindered their use in constructing whole embryo models, particularly post-implantation embryoids. Here, we establish a stepwise induction protocol to generate trophectoderm-like cells from mouse EPS cells.
Read the full summary ↓
These cells retain trophectoderm-specific transcriptomic features and can differentiate into trophoblast lineages in vivo. Moreover, combining these trophectoderm-like cells with EPS cell-derived primitive endoderm/epiblast bilineage structures enabled the robust generation of post-implantation embryoids in a transgene-free manner. EPS-derived embryoids recapitulate key developmental events of post-implantation mouse embryos, including the formation of the pro-amniotic cavity, anterior-posterior axis, primitive streak, gastrulation, and complex extraembryonic tissues. Notably, single-cell transcriptomic analysis revealed a high degree of transcriptional similarity between EPS-derived embryoids at day 6 and natural E7.5 mouse embryos. Our study presents a novel platform for modeling post-implantation mouse embryogenesis in vitro.
Published in
Trophectoderm-like cells from EPS cells enable generating EPS cell-derived post-implantation embryoids that complete gastrulation
Wang X, Cheng R, Wu C et al. · Protein & cell 2026 · PMID 40808575 · doi:10.1093/procel/pwaf059
This dataset
Open GSE291068 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 GSE291068_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1231499 and SRA study SRP567879. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40808575) ↗
Study design
16 conditions, mostly in duplicate
EPS ×4 EPS-N ×2 EPS-C3 ×2 EPS-C6 ×2 EPS-C10 ×2 EPS-C20 ×2 FAXY-TS ×2 FBS-TS ×2 +8 more

Supports a between-group comparison across 34 samples.

How we read this: 16 replicated groups read from 34 sample titles; they account for 34 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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