GEO series

Transcription factor NFYA directs male meiotic entry by facilitating accessible chromatin at the promoters of genes expressed during meiosis [scRNA-seq & scATAC-seq]

GSE296438 Mus musculus (mouse) Single-cell RNA-seq 10 samples Submitted 2025/05/10 Platform GPL34290

At a glance

Single-cell RNA-seq · mouse · 10 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: 10 samples: 10 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.
Paper: Transcription factor NFYA directs male meiotic entry by regulating accessible chromatin at meiotic promoters in miceThe EMBO journal · 2026

Summary (written by the submitters)

Meiotic prophase I characterized by homologous recombination and synapsis is an intricate step for spermatogenesis. This process entails extensive changes to chromatin and transcription. Recent studies have revealed that prior to prophase I, accessible chromatin bound by paused Pol II at meiotic gene promoters is essential for their timely activation during later stages of prophase I.

Read the full summary ↓

However, the factor responsible for promoting accessible chromatin at meiotic gene promoters before entry into prophase I is unknown. Here, we discovered that NFYA expressed in pre-meiotic germ cells promotes accessible chromatin at meiotic gene promoters. Concordantly, conditional germline deletion of Nfya in male mice blocks meiotic entry. Functionally, our spatial and single-cell ATAC-seq data revealed that loss of NFYA in pre-meiotic cells disrupts accessible chromatin at meiotic gene promoters. Our study identifies a pioneer role for NFYA in facilitating permissive chromatin at meiotic gene promoters before meiosis, thereby controlling the timely activation of meiotic genetic program during later meiosis.

Published in

Transcription factor NFYA directs male meiotic entry by regulating accessible chromatin at meiotic promoters in mice

Säflund M, Askari M, Eghbali A et al. · The EMBO journal 2026 · PMID 41857150 · doi:10.1038/s44318-026-00756-6

This dataset

Open GSE296438 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 GSE296438_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 PRJNA1254472 and SRA study SRP580686. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41857150) ↗

Study design

10 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 10 sample titles: 10 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

GSM8970449 Mus musculus Testis 11dpp single-cell RNA-seq
GSM8970450 Mus musculus Testis 17dpp single-cell RNA-seq
GSM8970451 Mus musculus Testis 25dpp single-cell RNA-seq
GSM8970452 Mus musculus Testis 11dpp single-cell ATAC-seq
GSM8970453 Mus musculus Testis 17dpp single-cell ATAC-seq
GSM8970454 Mus musculus Testis 25dpp single-cell ATAC-seq
GSM8970455 Mus musculus Testis NFYA_CKO_single-cell ATAC-seq
GSM8970456 Mus musculus Testis Cre_single-cell ATAC-seq
GSM8970457 Mus musculus Testis NFYA_CKO_single-cell RNA-seq
GSM8970458 Mus musculus Testis Cre_single-cell RNA-seq

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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.