← BioTransfer GEO Dataset Finder
GEO series

Broad H3K4me3 domains support oocyte genome silencing and maturation but are dispensable for repression in early embryos

GSE309712 Mus musculus (mouse) Single-cell RNA-seq 35 samples Submitted 2025/10/01 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 35 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
35 samples: 5 conditions, mostly with about 10 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
Broad H3K4me3 domains support oocyte genome silencing and maturation but are dispensable for repression in early embryosDevelopment (Cambridge, England) · 2025
Summary (written by the submitters)
To investigate whether demethylation of broad histone H3 lysine 4 trimethyl (H3K4me3) domains is sufficient to trigger premature embryonic genome activation (EGA), we overexpressed the H3K4me3 demethylase KDM5B in mouse zygotes and early 2-cell (2C) embryos via mRNA injection. We performed single-cell RNA sequencing (scRNA-seq) using the SMART-Seq Stranded Kit (Takara Bio) on individual Kdm5b-yfp–injected and water-injected control zygotes and 2C embryos.
Read the full summary ↓
Differential expression analysis revealed minimal transcriptional changes, and developmental stage, rather than KDM5B overexpression, accounted for most gene expression variance. Our findings demonstrate that wide-scale removal of H3K4me3 in zygotes or early 2C embryos is not sufficient to induce premature EGA, suggesting that genome silencing at these stages does not depend on broad H3K4me3 domains.
Published in
Broad H3K4me3 domains support oocyte genome silencing and maturation but are dispensable for repression in early embryos
Skuland T, Fosslie M, Khodeer S et al. · Development (Cambridge, England) 2025 · PMID 41143332 · doi:10.1242/dev.204638
This dataset
Open GSE309712 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 GSE309712_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 PRJNA1336783 and SRA study SRP630122. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41143332) ↗
Study design
5 conditions, mostly with about 10 replicates each
Ctrl water zygote, biol ×10 Kdm5b zygote, biol ×10 Ctrl water 2C, biol ×6 Kdm5b 2C, biol ×5 Ctrl water 2C, three blastomeres from differe… ×2 Ctrl water 2C, two blastomeres from different… ×1 Kdm5b 2C, three blastomeres from different em… ×1

Supports a between-group comparison across 33 samples.

How we read this: 5 replicated groups read from 35 sample titles; they account for 33 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

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.