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Androgen activity in the male embryonic hindbrain drives lethal PFA ependymoma [mm_MF_Dev_scRNA_batch2]

GSE311731 Mus musculus (mouse) Single-cell RNA-seq 30 samples Submitted 2026/03/25 Platform GPL34290
At a glance

Single-cell RNA-seq · mouse · 30 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
30 samples: 14 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
Androgen activity in the male embryonic hindbrain drives lethal PFA ependymomaNature · 2026
Summary (written by the submitters)
In this study, we examine transcriptional sex differences between developing male and female hindbrain cells and their role in PFA pathogenesis, primarily in the poor prognosis of male patients.
Published in
Androgen activity in the male embryonic hindbrain drives lethal PFA ependymoma
Zhang J, Ong W, Rasnitsyn A et al. · Nature 2026 · PMID 41882358 · doi:10.1038/s41586-026-10264-6
This dataset
Open GSE311731 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 GSE311731_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 PRJNA1370843 and SRA study SRP649689. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41882358) ↗
Study design
14 conditions, mostly in duplicate
Mouse_hindbrain_E10_female ×2 Mouse_hindbrain_E10_male ×2 Mouse_hindbrain_E11_female ×2 Mouse_hindbrain_E11_male ×2 Mouse_hindbrain_E12_female ×2 Mouse_hindbrain_E12_male ×2 Mouse_cerebellum_E13_female ×2 Mouse_cerebellum_E13_male ×2 +8 more

Supports a between-group comparison across 28 samples.

How we read this: 14 replicated groups read from 30 sample titles; they account for 28 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
Datasets on a similar topic

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