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Single-cell exploration of gonadal somatic cell lineage specification during human sex determination

GSE288161 Homo sapiens (human) Single-cell RNA-seq 20 samples Submitted 2025/09/02 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 20 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Homo sapiens (human)
Samples
20 samples: 10 × Fetal Testis, XY, DMSO, EH vs 10 × Fetal Testis, XY, Leuprolide, EHGroups 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
Single-cell exploration of gonadal somatic cell lineage specification during human sex determinationDevelopmental cell · 2026
Summary (written by the submitters)
Gonad development is an exciting model to study cell fate commitment. A better understanding of sex determination requires the identification of all involved cell types and their dynamic expression programs. Here, we present an atlas of 128,000 single cells from human gonads between 5 and 12 post-conceptional weeks. A focused analysis of somatic cells uncovered a population of bipotential progenitors derived from the coelomic epithelium of both testes and ovaries, which may have the capacity to commit to either a steroidogenic or a supporting fate.
Read the full summary ↓
Moreover, our analyses suggest that early supporting cells, prior to differentiation into Sertoli or pre-granulosa cells, also give rise to the rete testis/ovarii and that the ovary retains the capacity to feed the supporting cell pool for an extended period of time, directly from the surface epithelium. Finally, the potential involvement of the gonadotropin releasing hormone (GnRH) signaling pathway in regulating testis differentiation was assessed ex vivo.
Published in
Single-cell exploration of gonadal somatic cell lineage specification during human sex determination
Lardenois A, Suglia A, Moore CL et al. · Developmental cell 2026 · PMID 41072414 · doi:10.1016/j.devcel.2025.09.011
This dataset
Open GSE288161 in finder → Find more human 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 GSE288161_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 PRJNA1216299. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41072414) ↗
Study design
10 × Fetal Testis, XY, DMSO, EH vs 10 × Fetal Testis, XY, Leuprolide, EH

Supports a between-group comparison across 20 samples.

How we read this: 2 replicated groups read from 20 sample titles; they account for 20 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
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