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Z-DNA formation induces the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization

GSE291992 Mus musculus (mouse) DNA methylation 47 samples Submitted 2025/12/11 Platform GPL19057Platform GPL18573Platform GPL30172
At a glance

DNA methylation · mouse · 47 samples

What it is
DNA methylationChemical marks on DNA that help switch genes on or off.
Organism
Mus musculus (mouse)
Samples
47 samples: 13 conditions, mostly in duplicateGroups 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
Z-DNA formation regulates the totipotent-like state and primes Zscan4-dependent chromatin compartmentalizationNature structural & molecular biology · 2026
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Z-DNA formation regulates the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization
Shajahan S, Loe-Mie Y, Asselin L et al. · Nature structural & molecular biology 2026 · PMID 41703099 · doi:10.1038/s41594-026-01751-5
This dataset
Open GSE291992 in finder → Find more 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 GSE291992_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 beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA1236291 and SRA study SRP570470. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41703099) ↗
Study design
13 conditions, mostly in duplicate
2CLC-siCtrl ×3 methyl-seq_2C ×3 methyl-seq_ESC ×3 2CLC-curaxin ×2 2CLC-DFMO-AMXT-24 ×2 2CLC-DFMO-AMXT-48 ×2 2CLC ×2 2CLC-siZscan4 ×2 +23 more

Supports a between-group comparison across 29 samples.

How we read this: 13 replicated groups read from 47 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

+ 7 more — browse all 47 samples with per-sample file links →

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