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Transcriptomic Signatures of WNT-Driven Pathways and Granulosa Cell-Oocyte Interaction during Primordial Follicle Activation

GSE255212 Mus musculus (mouse) Single-cell RNA-seq 762 samples Submitted 2024/10/01 Platform GPL19057
At a glance

Single-cell RNA-seq · mouse · 762 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
762 samples: 35 conditions, mostly with about 12 replicates eachGroups 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
Transcriptomic signatures of WNT-driven pathways and granulosa cell-oocyte interactions during primordial follicle activationPloS one · 2024
Summary (written by the submitters)
Primordial follicle activation (PFA) is a pivotal event in female reproductive biology, orchestrating the transition from quiescent to growing follicles. This study employed comprehensive single-cell RNA sequencing to investigate the transcriptomic landscape of ovarian cells, focusing on the process of PFA. The aim of our study was to gain insights into the detailed regulatory mechanisms governing synchronized dormancy and activation between granulosa cells (GCs) and oocytes with decomposition of the PFA process.
Read the full summary ↓
The Wntless (Wls) conditional knockout (cKO) mouse served as a unique model, suppressing the transition from pre-GC to GC, and disrupting somatic cell-derived WNT signaling in the ovary. Our data revealed immediate transcriptomic changes in GCs post-PFA in Wls cKO mice, leading to a divergent trajectory, while oocytes exhibited modest transcriptomic alterations. Subpopulation analysis identified molecular pathways affected by WNT signaling on GC maturation, along with specific gene signatures linked to dormant and activated oocytes. Despite minimal evidence of continuous up-regulation of dormancy-related genes in oocytes, loss of WNT signaling in (pre-)GCs impacted gene expression on oocytes even before PFA, subsequently influencing them globally. The infertility observed in Wls cKO mice was attributed to compromised GC-oocyte molecular crosstalk and a microenvironment for oocytes. Our study highlights the pivotal role of the WNT-signaling pathway and its molecular signature, emphasizing the importance of intercellular crosstalk between (pre-)GCs and oocytes in orchestrating folliculogenesis.
Published in
Transcriptomic signatures of WNT-driven pathways and granulosa cell-oocyte interactions during primordial follicle activation
Takase HM, Mishina T, Hayashi T et al. · PloS one 2024 · PMID 39441825 · doi:10.1371/journal.pone.0311978
This dataset
Open GSE255212 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 GSE255212_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 PRJNA1073960 and SRA study SRP488523. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39441825) ↗
Study design
35 conditions, mostly with about 12 replicates each
mGCCtrl_HMD201207001_BA ×12 mGCCtrl_HMD201207001_AI ×12 mGCCtrl_HMD201207001_CL ×12 mGCCtrl_HMD201207001_CH ×12 mGCCtrl_HMD201207001_BI ×12 mOCCtrl_HMD201207001_DB ×12 mGCCtrl_HMD201207001_CB ×12 mGCCtrl_HMD201207001_AE ×12 +40 more

Supports a between-group comparison across 387 samples.

How we read this: 35 replicated groups read from the first 400 of 762 sample titles; they account for 387 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

+ 722 more — browse all 762 samples with per-sample file links →

Datasets on a similar topic

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