GEO series

Long-term live imaging reveals sexual dimorphism in the stem cell hierarchy of mouse epidermis

GSE294042 Mus musculus (mouse) Single-cell RNA-seq 6 samples Submitted 2026/08/07 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 6 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: 6 samples: 2 × IFE basal cells male vs 2 × IFE basal cells female vs 2 × IFE basal cells castrated maleGroups 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.

Summary (written by the submitters)

The epidermis is a stratified epithelium comprising proliferative basal cells and differentiated suprabasal cells that are continuously renewed throughout life. Conflicting theories have been proposed regarding the heterogeneity of basal cell layer, with some studies proposing that all proliferative cells have self-renewal potential during homeostasis while others posit a model in which stem cell differentiation occurs through an intermediate progenitor state with strictly limited proliferative potential.

Read the full summary ↓

To elucidate the heterogeneity and pattern of cell fate, we performed intravital timelapse imaging to track the fate of individual lineage-labeled cells over the long term in the ear skin interfollicular epidermis. Quantitative analysis of clonal dynamics supports a two-compartment model of epidermal homeostasis, with basal cells organized in a stem-progenitor cell hierarchy. Critical to these conclusions was the discovery of a sexual dimorphism in epidermal fate, with female mice showing a highly synchronized pattern of differentiation and delamination. Single-cell RNA sequencing, transcriptional profiling, and clonal analysis following castration revealed that male sex hormones promote SC differentiation and delamination. As well as providing insight into the functional identity of the SC population during homeostasis, our study highlights sex-specific differences in the regulation of epidermal stem and progenitor cell fate.

This dataset

Open GSE294042 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 GSE294042_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 PRJNA1247949 and SRA study SRP577208. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

2 × IFE basal cells male vs 2 × IFE basal cells female vs 2 × IFE basal cells castrated male

Supports a between-group comparison across 6 samples.

How we read this: 3 replicated groups read from 6 sample titles; they account for 6 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

GSM8897183 IFE basal cells male 1 IFE basal cells male
GSM8897184 IFE basal cells male 2 IFE basal cells male
GSM8897185 IFE basal cells female 1 IFE basal cells female
GSM8897186 IFE basal cells female 2 IFE basal cells female
GSM8897187 IFE basal cells castrated male 1 IFE basal cells castrat…
GSM8897188 IFE basal cells castrated male 2 IFE basal cells castrat…

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