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Single-nucleus chromatin accessibility landscape in mouse preimplantation embryos

GSE282209 Mus musculus (mouse) Single-nucleus RNA-seq 12 samples Submitted 2026/01/13 Platform GPL21273
At a glance

Single-nucleus RNA-seq · mouse · 12 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue).
Organism
Mus musculus (mouse)
Samples
12 samples: 12 samples, each with a distinct title — no replicated groupsGroups 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.
Summary (written by the submitters)
The initiation of mammalian life begins with fertilization, when terminally committed gametes are reprogrammed into a totipotent state. However, the mechanisms of chromatin reorganization within a single-nucleus during this reprogramming remain shrouded in mystery. Here we developed a single-nucleus assay for transposase-accessible chromatin with high throughput sequencing (snATAC-seq) for preimplantation embryos, and profiling over 3,000 blastomeres from oocyte to blastocyst.
Read the full summary ↓
We observed dramatic dynamics in chromatin accessibility from the zygote to the 2-cell stage, corresponding to a crucial event in preimplantation development: zygotic genome activation (ZGA). To date, only a handful of transcription factors (TFs) involved in ZGA regulation have been identified. Surprisingly, we discovered 148 significantly enriched ZGA-specific TFs, with nearly all well-studied ZGA regulators including Obox, Nr5a2, Zscan4, and Dux. Notably, accessible chromatin extensively overlaps with transposable elements, particularly B1, which contains numerous binding motifs for TFs associated with ZGA regulation. And a de novo TF family, "AT-rich interactive domain" (ARID), were significantly enriched in both accessible chromatin and B1 in ZGA stages. Taken together, our study offered the first highly sensitive single-nuclear chromatin accessibility maps of mouse preimplantation embryos and provided new insights into the programmatic regulation between cis-elements and trans-regulators in this process.
This dataset
Open GSE282209 in finder → Find more mouse ChIP / ATAC / CUT&Tag 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 GSE282209_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 PRJNA1187588 and SRA study SRP546045. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
12 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 12 sample titles: 12 distinct titles with little repetition. 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 ChIP / ATAC / CUT&Tag datasets in GEO →

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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.