GEO series

PI3K/AKT signalling regulates mouse Inner Cell Mass (ICM) progenitor specification [scRNA-seq]

GSE234578 Mus musculus (mouse) Single-cell RNA-seq 186 samples Submitted 2024/10/25 Platform GPL21626

At a glance

Single-cell RNA-seq · mouse · 186 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 186 samples
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: PI3K/AKT signaling controls ICM maturation and proper epiblast and primitive endoderm specification in miceDevelopmental cell · 2025

Summary (written by the submitters)

The inner cell mass (ICM) of early mouse embryos is specified into Epiblast (Epi) and primitive endoderm (PrE) lineages during blastocyst formation. The antagonistic transcription factors (TFs) NANOG and GATA6 in combination with FGF/ERK signaling are central actors in ICM fate choice. However, what initiates the specification of the bipotent ICM progenitor and whether other factors are involved in this process is not fully understood yet.

Read the full summary ↓

Here, we report the key role of PI3K in mouse ICM progenitors specification. Surprisingly, while the PI3K/AKT signaling pathway is known for almost two decades to participate to the maintenance of pluripotency in stem cells, no role for this pathway in ICM cell fate decisions has been reported so far. This is likely due to the dynamic and asynchronous nature of ICM specification combined with the pleiotropic and rapidly evolving functions mediated by PI3K/AKT. By limiting the perturbations of the pathway to a short time-window corresponding to the early phase of ICM specification, we unravelled a dual role of PI3K in ICM progenitor, being required on the one hand for the maintenance of pluripotency TFs and, on the other hand, for the competence to engage into PrE differentiation in response to FGF signaling. Thus, our work identifies PI3K as a novel critical regulator of ICM progenitor specification in the mouse embryo.

Published in

PI3K/AKT signaling controls ICM maturation and proper epiblast and primitive endoderm specification in mice

Geiselmann A, Micouin A, Vandormael-Pournin S et al. · Developmental cell 2025 · PMID 39461340 · doi:10.1016/j.devcel.2024.10.001

This dataset

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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 GSE234578_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 PRJNA982080 and SRA study SRP442030. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39461340) ↗

Samples in this study

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+ 186 more — browse all 186 samples with per-sample file links →

Datasets on a similar topic

GSE265767 PI3K/AKT signalling regulates mouse Inner Cell Mass (ICM) progenitor specification [FLASH-seq] 26 samples shares pi3k, akt, icm, specification, progenitor, inner, mass
GSE286925 In vitro PI3Kδ inhibition skews CD8 T cell differentiation towards progenitor exhaustion in vivo and reprograms tumor microenvironment metabolism, immune composition, and inflammation [scRNA-seq] 12 samples shares pi3k, progenitor, scrna-seq
GSE288213 Altered pathways in Cockayne syndrome: Involvement of MAPK, PI3K-Akt, extracellular matrix, inflammation, and neuronal signaling 30 samples shares pi3k, akt
GSE305628 Isobavachalcone ameliorates TNBS-induced Crohn’s disease-like colitis via GPR84-PI3K-AKT axis 18 samples shares pi3k, akt
GSE308218 Protective effects of swimming exercises on murine tumor-induced cardiac inflammation and apoptosis by suppressing PI3K-AKT pathway 17 samples shares pi3k, akt
GSE304488 EET Reduction Contributes to Granulosa Cell Senescence And Endometriosis-Associated Infertility Via the PI3K/AKT/mTOR Signaling Pathway 16 samples shares pi3k, akt
GSE201806 Harmful algal bloom toxin microcystin-LR interferes with PP1-mediated PI3K/AKT/FOXO1 signaling in granulosa cells to disrupt ovarian follicle maturation and ovulation 15 samples shares pi3k, akt
GSE307180 Transcriptomic analysis and experimental verification reveal the involvement of PI3K/AKT signaling pathway in high-altitude cognitive dysfunction [6_OHG] 13 samples shares pi3k, akt

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