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Preventing CpG hypermethylation in oocytes safeguards mouse development

GSE234968 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 612 samples Submitted 2025/03/27 Platform GPL19057Platform GPL24247Platform GPL17021
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 612 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Mus musculus (mouse)
Samples
612 samples: 18 conditions, mostly with about 20 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
Preventing CpG hypermethylation in oocytes safeguards mouse developmentDevelopmental cell · 2025
Summary (written by the submitters)
Except for regulatory CpG-island sequences, genomes of most mammalian cells are widely DNA-methylated. In oocytes though, DNAme is largely confined to transcribed regions. The mechanisms restricting de novo DNAme in oocytes and the relevance thereof for zygotic genome activation and embryonic development are largely unknown. Here we show that KDM2A and KDM2B, two histone demethylases, prevent genome-wide accumulation of histone H3 lysine 36 di-methylation, thereby impeding DNMT3A-catalyzed DNAme.
Read the full summary ↓
We demonstrate that aberrant DNAme at CpG-islands inherited from Kdm2a/Kdm2b double mutant oocytes represses gene transcription in two-cell embryos. Aberrant maternal DNAme impairs pre-implantation embryonic development which is suppressed by Dnmt3a deficiency during oogenesis. Hence, KDM2A/KDM2B are essential for confining the oocyte methylome, thereby conferring competence for early embryonic development. Our research implies that the reprogramming capacity eminent to early embryos is insufficient for erasing aberrant DNAme from maternal chromatin, and that early development is vulnerable to gene dosage haplo-insufficiency effects.
Published in
Preventing CpG hypermethylation in oocytes safeguards mouse development
Kawamura YK, Ozonov EA, Papasaikas P et al. · Developmental cell 2025 · PMID 40902605 · doi:10.1016/j.devcel.2025.08.005
This dataset
Open GSE234968 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 GSE234968_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA983810 and SRA study SRP607431. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40902605) ↗
Study design
18 conditions, mostly with about 20 replicates each
GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO ×30 GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC ×29 GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO ×29 GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC ×26 GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC ×24 GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO ×24 GVO_scRNA_Ctrl.Ring1_KO.Rnf2_KO ×23 GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC ×22 +10 more

Supports a between-group comparison across 400 samples.

How we read this: 18 replicated groups read from the first 400 of 612 sample titles; they account for 400 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

+ 572 more — browse all 612 samples with per-sample file links →

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