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Generation of germinal-vesicle oocytes from mouse embryonic stem cells under an ovarian soma-free condition (SC3-Seq)

GSE272450 Mus musculus (mouse) RNA-seq (gene expression) 156 samples Submitted 2025/05/19 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 156 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
156 samples: 156 samples, each with a distinct title — no replicated groupsGroups 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
Generation of germinal-vesicle oocytes from mouse embryonic stem cells under an ovarian soma-free conditionDevelopmental cell · 2025
Summary (written by the submitters)
In vitro oogenesis provides a platform to elucidate the mechanism of oocyte development and advance reproductive medicine. The prevalent in vitro oogenesis model requires ovarian somatic cells (OSCs) to support oocyte development, yet complex three-dimensional oocyte–OSC interactions pose difficulties in systems regulation and mechanistic understanding.
Read the full summary ↓
Here, we present an OSC-free system of in vitro oogenesis: upon optimized provision of retinoic acid and bone morphogenetic protein on feeders, mouse primordial germ cell-like cells induced from embryonic stem cells propagate robustly, and enter/progress through meiotic prophase I, generating abundant fetal oocyte-like cells at diplotene arrest. With key cytokines, signaling activators, and antioxidants, they show prominent growth and differentiate into cells comparable to germinal-vesicle oocytes in morphology, transcriptome, and histone-modification profiles, with competence to resume meiosis with germinal-vesicle breakdown. By reconstituting major phases of oogenesis with minimal components, our study creates a foundation for OSC-free in vitro oogenesis in mammals, including humans.
Published in
Generation of germinal-vesicle oocytes from mouse embryonic stem cells under an ovarian soma-free condition
Nosaka Y, Nagano M, Yabuta Y et al. · Developmental cell 2025 · PMID 40592343 · doi:10.1016/j.devcel.2025.06.008
This dataset
Open GSE272450 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 GSE272450_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 PRJNA1136899 and SRA study SRP520534. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40592343) ↗
Study design
156 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 156 sample titles: 156 distinct titles with little repetition. 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

+ 116 more — browse all 156 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.