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Vitrification preserves oocyte transcriptome in a 3D in vitro follicle development and oocyte maturation system

GSE292062 Mus musculus (mouse) Single-cell RNA-seq 32 samples Submitted 2025/04/02 Platform GPL34290
At a glance

Single-cell RNA-seq · mouse · 32 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
32 samples: 12 × MII oocyte from post-hCG fresh follicle, biol vs 12 × MII oocyte from post-hCG vitrified follicle, biol vs 4 × GV oocyte from day 8 fresh follicle, biol vs 4 × GV oocyte from day 8 vitrfied follicle, biolGroups 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
Vitrification preserves oocyte transcriptome in a 3D in vitro follicle development and oocyte maturation system†Biology of reproduction · 2025
Summary (written by the submitters)
Vitrification is increasingly used to cryopreserve gametes and embryos in assisted reproductive technology (ART). Our prior research demonstrates that vitrification preserves the viability and functionality of ovarian follicles. However, its impact on follicle-enclosed oocyte remains unknown. The current study investigates whether vitrification, combined with a 3D encapsulated in vitro follicle growth (eIVFG) system, maintains oocyte transcriptome during in vitro follicle development and oocyte maturation.
Read the full summary ↓
Immature mouse preantral follicles were vitrified and cultured in eIVFG for 8 days to grow to the preovulatory stage, followed with the induction of ovulation and oocyte maturation on day 9, with fresh follicles as the control. Oocytes at germinal vesicle (GV) stage from grown preovulatory follicles on day 8 and oocytes at metaphase II (MII) upon ovulation on day 9 were collected for single-oocyte Smart-Seq2 RNA sequencing analysis. The principal component analysis (PCA) separated GV and MII oocytes into two distinct clusters, but oocytes from fresh and vitrified follicles were largely overlapped. Differential gene expression (DEG) analysis revealed that GV or MII oocytes from fresh and vitrified follicles had comparable expression of maternal effect genes and other genes related to oocyte meiotic and developmental competence. There was a significant transcriptomic change during the GV-to-MII transition. Gene ontology (GO) and KEGG analysis identified DEGs between GV and MII oocytes related to cell cycle, RNA processing, mitochondria, and ribosome. In summary, our study demonstrates that vitrification preserves oocyte transcriptome during in vitro follicle development and oocyte maturation, supporting its potential in fertility preservation. Moreover, our single-oocyte RNA sequencing analysis identifies key DEGs upon GV-to-MII transition, indicating their potential functions in underpinning oocyte meiotic and developmental competence.
Published in
Vitrification preserves oocyte transcriptome in a 3D in vitro follicle development and oocyte maturation system†
Zhang J, Zhao W, Cheron S et al. · Biology of reproduction 2025 · PMID 40273426 · doi:10.1093/biolre/ioaf097
This dataset
Open GSE292062 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 GSE292062_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 PRJNA1236483 and SRA study SRP570604. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40273426) ↗
Study design
12 × MII oocyte from post-hCG fresh follicle, biol vs 12 × MII oocyte from post-hCG vitrified follicle, biol vs 4 × GV oocyte from day 8 fresh follicle, biol vs 4 × GV oocyte from day 8 vitrfied follicle, biol

Supports a between-group comparison across 32 samples.

How we read this: 4 replicated groups read from 32 sample titles; they account for 32 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
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