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Establishing competence for trophectoderm specification in mouse embryos before the first lineage bifurcation [RNA-seq]

GSE284144 Mus musculus (mouse) RNA-seq (gene expression) 22 samples Submitted 2025/10/24 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 22 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
22 samples: 11 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
Role of CEBPa in trophectoderm competence installmentScience advances · 2025
Summary (written by the submitters)
How embryonic blastomeres transition from totipotency to differentiation remains a fundamental question in developmental biology. Here, we uncover the transcription factor CEBPa as an orchestrator of this process. CEBPa expression is first activated by NR5A2 at the 2-cell to 4-cell transition and in a second wave peaks in the trophectoderm of blastocysts.
Read the full summary ↓
Loss of CEBPa disrupts timely blastocyst formation and impairs trophectoderm development, while its forced expression in embryonic stem cells drives differentiation into trophectoderm-like cells. Mechanistically, CEBPa sequentially activates key trophectoderm enhancers in a dose-dependent manner. At the 4-cell stage, some of these trophectoderm enhancers are already active while others are primed or still closed, placing blastomeres in a state of alert. These findings establish CEBPa as a molecular switch that equips 4-cell blastomeres with the competence for trophectoderm differentiation, defining the earliest steps in cell fate bifurcation and shedding new light on the mechanisms driving embryonic lineage specification.
Published in
Role of CEBPa in trophectoderm competence installment
Wei X, Salvador-Martinez I, Meglicki M et al. · Science advances 2025 · PMID 41313781 · doi:10.1126/sciadv.ady1693
This dataset
Open GSE284144 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 GSE284144_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 PRJNA1197454 and SRA study SRP551179. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41313781) ↗
Study design
11 conditions, mostly in duplicate
Embryonic stem cells, ×2 ESC, CEBPa induced, 12h, clone ×2 ESC, CEBPa induced, 24h, clone ×2 ESC, CEBPa induced, 48h, clone ×2 ESC, CEBPa induced, 72h, clone ×2 Trophoblast stem cells, ×2 ESC, CEBPa non-induced, 0h, clone ×2 ESC, CEBPa induced, 48h, sorted SSEA1+, clone ×2 +3 more

Supports a between-group comparison across 22 samples.

How we read this: 11 replicated groups read from 22 sample titles; they account for 22 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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