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Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates

GSE166226 Mus musculus (mouse) Single-cell RNA-seq 615 samples Submitted 2025/05/31 Platform GPL17021Platform GPL13112
At a glance

Single-cell RNA-seq · mouse · 615 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
615 samples: 24 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
Scaling and self-similarity in the formation of the embryonic epigenomeNature physics · 2026
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Scaling and self-similarity in the formation of the embryonic epigenome
Olmeda F, Lohoff T, Kafetzopoulos I et al. · Nature physics 2026 · PMID 42318073 · doi:10.1038/s41567-026-03263-x
This dataset
Open GSE166226 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 GSE166226_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 PRJNA699614 and SRA study SRP304188. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42318073) ↗
Study design
24 conditions, mostly with about 12 replicates each
D0_A ×12 D0_B ×12 D0_C ×12 D0_D ×12 D0_E ×12 D0_F ×12 D0_G ×12 D0_H ×12 +128 more

Supports a between-group comparison across 288 samples.

How we read this: 24 replicated groups read from the first 400 of 615 sample titles; they account for 288 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

+ 575 more — browse all 615 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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