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Molecular Signatures and Signaling Interactions of the Hair Follicle Stem Cell Niche

GSE300176 Mus musculus (mouse) Single-cell RNA-seq 56 samples Submitted 2025/12/15 Platform GPL13112
At a glance

Single-cell RNA-seq · mouse · 56 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
56 samples: 28 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
Molecular signatures and signaling interactions of the hair follicle stem cell nicheThe Journal of investigative dermatology · 2026
Summary (written by the submitters)
Signaling interactions between the dermal papilla (DP) and neighboring stem cells in the hair germ (HGSCs) and bulge (BuSCs) regulate new follicle growth in the hair cycle. To study these interactions, the three populations had been profiled together by now-outdated microarrays or separately by bulk RNA-sequencing. Recent single-cell transcriptomics established signatures of DP, BuSCs and HGSCs, but low detection sensitivity limited the depth of gene expression discovery.
Read the full summary ↓
Here, we define the transcriptomes of DP, BuSCs, HGSCs, epidermal, follicle and dermal fibroblast cells – after flow-sorting each population from four neighboring mouse back skin regions – to gain deeper insights into the unique gene expression programs of SCs and their instructive niche. With cross-comparisons of 56 whole-transcriptome measurements, we classify cell type-specific molecular signatures of enriched genes with unprecedented sensitivity. Joint analysis with signatures from 15 leading studies published in the last 20 years revealed many previously undescribed DP, BuSC and HGSC genes in mouse and human counterparts. With ligand-receptor mapping and CellChat analyses we then uncover comprehensive cell-cell communication insights. Finally, we provide a new installment of our Hair-Gel repository along with numerous signature and other gene tables for easy exploration of gene expression in hair follicle SCs and their niche.
Published in
Molecular signatures and signaling interactions of the hair follicle stem cell niche
Ghuwalewala S, Cao J, Rezza A et al. · The Journal of investigative dermatology 2026 · PMID 41407191 · doi:10.1016/j.jid.2025.11.021
This dataset
Open GSE300176 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 GSE300176_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 PRJNA1279173 and SRA study SRP593017. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41407191) ↗
Study design
28 conditions, mostly in duplicate
P22_Neg_Zone1 ×2 P22_Neg_Zone2 ×2 P22_Neg_Zone3 ×2 P22_Neg_Zone4 ×2 P22_DF_Zone1 ×2 P22_DF_Zone2 ×2 P22_DF_Zone3 ×2 P22_DF_Zone4 ×2 +20 more

Supports a between-group comparison across 56 samples.

How we read this: 28 replicated groups read from 56 sample titles; they account for 56 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

+ 16 more — browse all 56 samples with per-sample file links →

Datasets on a similar topic

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