GEO series

Transcriptional changes of spermatogenic cells by Tex10 deficiency

GSE288152 Mus musculus (mouse) Single-cell RNA-seq 16 samples Submitted 2025/02/01 Platform GPL21103

At a glance

Single-cell RNA-seq · mouse · 16 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Mus musculus (mouse)
Samples: 16 samples: 8 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: Pluripotency factor Tex10 finetunes Wnt signaling for spermatogenesis and primordial germ cell developmentNature communications · 2025

Summary (written by the submitters)

Testis-specific transcript 10 (Tex10) is highly expressed in the testis, embryonic stem cells (ESCs), and primordial germ cells (PGCs). We previously generated a Tex10 knockout mouse model demonstrating its critical roles in ESC pluripotency and preimplantation development. Here, using conditional knockout mice and dTAG-degron ESCs, we show Tex10 is required for spermatogenesis and ESC-to-PGCLC differentiation.

Read the full summary ↓

Specifically, Tex10-null spermatocytes arrest at metaphase I, compromising round spermatid formation. Tex10 depletion and overexpression compromise and enhance ESC-to-PGCLC differentiation, respectively. Mechanistically, bulk and single-cell RNA sequencing reveals that Tex10 depletion downregulates genes involved in pluripotency, PGC development, and spermatogenesis while upregulating genes promoting somatic programs. Chromatin occupancy study reveals that Tex10 binds to H3K4me3-marked promoters of Psmd3 and Psmd7, negative regulators of Wnt signaling, and activates their expression, thereby restraining Wnt signaling. Our study identifies Tex10 as a previously unappreciated factor in spermatogenesis and PGC development, offering potential therapeutic insights for treating male infertility.

Published in

Pluripotency factor Tex10 finetunes Wnt signaling for spermatogenesis and primordial germ cell development

Yuan F, Yang J, Ma F et al. · Nature communications 2025 · PMID 39988597 · doi:10.1038/s41467-025-57165-2

This dataset

Open GSE288152 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 GSE288152_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 PRJNA1216288 and SRA study SRP560243. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39988597) ↗

Study design

8 conditions, mostly in duplicate

C_spg ×2 C_sctMI ×2 C_sctMII ×2 C_RS ×2 KO_spg ×2 KO_sctMI ×2 KO_sctMII ×2 KO_RS ×2

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 16 sample titles; they account for 16 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

GSM8760107 C_spg_rep1 C_spg
GSM8760108 C_sctMI_rep1 C_sctMI
GSM8760109 C_sctMII_rep1 C_sctMII
GSM8760110 C_RS_rep1 C_RS
GSM8760111 C_spg_rep2 C_spg
GSM8760112 C_sctMI_rep2 C_sctMI
GSM8760113 C_sctMII_rep2 C_sctMII
GSM8760114 C_RS_rep2 C_RS
GSM8760115 KO_spg_rep1 KO_spg
GSM8760116 KO_spg_rep2 KO_spg
GSM8760117 KO_sctMI_rep1 KO_sctMI
GSM8760118 KO_sctMI_rep2 KO_sctMI
GSM8760119 KO_sctMII_rep1 KO_sctMII
GSM8760120 KO_sctMII_rep2 KO_sctMII
GSM8760121 KO_RS_rep1 KO_RS
GSM8760122 KO_RS_rep2 KO_RS

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