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Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenetic maintenance

GSE232637 Mus musculus (mouse) Single-cell RNA-seq 42 samples Submitted 2025/08/21 Platform GPL30173Platform GPL18573Platform GPL30172
At a glance

Single-cell RNA-seq · mouse · 42 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Mus musculus (mouse)
Samples
42 samples: 7 conditions, mostly with about 4 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
Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenanceNature methods · 2025
Summary (written by the submitters)
DNA methylation and histone modifications encode epigenetic information. Recently, major progress was made to measure either mark at single-cell resolution. However, a method for simultaneous detection is lacking, preventing study of their interactions in complex systems. To bridge this gap, we developed scEpi2-seq. This technique provides single-molecule and single-cell readout of histone modifications and DNA methylation and reveals how DNA methylation maintenance is influenced by the local chromatin context.
Published in
Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance
Geisenberger C, van den Berg J, van Batenburg V et al. · Nature methods 2025 · PMID 40999097 · doi:10.1038/s41592-025-02847-4
This dataset
Open GSE232637 in finder → Find more methylation 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 GSE232637_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 PRJNA973084 and SRA study SRP438081. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40999097) ↗
Study design
7 conditions, mostly with about 4 replicates each
Mouse intestine animal 3 plate ×5 RPE-1 hTERT FUCCI H3K27me3 ×4 RPE-1 hTERT FUCCI H3K36me3 ×4 RPE-1 hTERT FUCCI H3K9me3 ×4 K562 H3K27me3 rep 2 plate ×4 Mouse intestine animal 1 plate ×4 Mouse intestine animal 2 plate ×4 K562 H3K27me ×1 +12 more

Supports a between-group comparison across 29 samples.

How we read this: 7 replicated groups read from 42 sample titles; they account for 29 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

+ 2 more — browse all 42 samples with per-sample file links →

Datasets on a similar topic

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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.