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Single nucleotide insertion within a remote enhancer causes XX mice to be born as males

GSE291809 Mus musculus (mouse) RNA-seq (gene expression) 46 samples Submitted 2026/02/21 Platform GPL34290
At a glance

RNA-seq (gene expression) · mouse · 46 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
46 samples: 12 conditions, mostly in triplicateGroups 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
A single-nucleotide enhancer mutation overrides chromosomal sex to drive XX male developmentNature communications · 2026
Summary (written by the submitters)
In this study, we show that mice carrying a 3 bp deletion or 1 bp insertion within the SOX9 BS of Enh13 are born as XX males. At adult stages, mice appear externally and internally as males but their testes are small and devoid of sperm due to the lack of the Y chromosomes. At embryonic stages, XX homozygous gonads appear as ovotestis at various severities with the 1 bp insertion appearing more as a testis.
Read the full summary ↓
Transcriptomic analysis of E12.5 gonads shows that indeed the XX homozygous gonads are positioned in between the testis and ovary while XY homozygous gonads are indistinguishable of wild type (WT) XY gonads. These findings implicate Enh13 as a dual regulatory element essential for both testicular and ovarian development, placing it at the critical intersection of sexual differentiation pathways.
Published in
A single-nucleotide enhancer mutation overrides chromosomal sex to drive XX male development
Abberbock E, Ridnik M, Stévant I et al. · Nature communications 2026 · PMID 41957362 · doi:10.1038/s41467-026-71328-9
This dataset
Open GSE291809 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 GSE291809_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1235272 and SRA study SRP569946. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41957362) ↗
Study design
12 conditions, mostly in triplicate
Whole gonad E12.5 XX Enh13-1bp-ins-hom ×5 Whole gonad E12.5 XX Enh13-3bp-12bp-del-hom ×5 Whole gonad E12.5 XX Enh13-3bp-del-hom ×5 Whole gonad E12.5 XY Enh13-1bp-ins-hom ×5 Whole gonad E12.5 XY Enh13-3bp-del-hom ×5 Whole gonad E12.5 XX Enh13-1bp-ins-het ×3 Whole gonad E12.5 XX Enh13-3bp-del-het ×3 Whole gonad E12.5 XX WT ×3 +4 more

Supports a between-group comparison across 46 samples.

How we read this: 12 replicated groups read from 46 sample titles; they account for 46 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

+ 6 more — browse all 46 samples with per-sample file links →

Datasets on a similar topic

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