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Identification of unique mesenchymal subpopulations for regenerating follicular and interfollicular epithelia after devastating necrosis in the skin graft

GSE273335 Mus musculus (mouse) Single-cell RNA-seq 34 samples Submitted 2025/08/13 Platform GPL19057Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 34 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
34 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
Identification of Keratin 5-Expressing Fibroblasts for Regenerating Keratinocytes in the Necrotic Skin GraftJID innovations : skin science from molecules to population health · 2025
Summary (written by the submitters)
We investigated chronological changes of the skin graft in mice for 15 days at single cell-transcriptomic levels. We found devastating necrotic changes in the dermal and epidermal tissues at post-operated day 3, (POD3), followed by significant regeneration processes of the follicular and interfollicular tissues after POD 6. Dermal papilla cells in the necrotic milieu exserted significant activation of Wnt signaling pathway and Sox2 and Fgf7 expressions, all of those are critical for follicular development in the fetal skin.
Read the full summary ↓
We further identified a unique mesenchymal subpopulation, which expressed keratinocyte-specific genes, such as Krt5 and Epcam, as well as Irf6, a transcriptional factor to induce mesenchymal to epithelial transition (MET). Our data revealed significant contribution of the unique mesenchymal cell populations for the follicular and interfollicular epithelial regeneration after severe necrosis in the skin graft.
Published in
Identification of Keratin 5-Expressing Fibroblasts for Regenerating Keratinocytes in the Necrotic Skin Graft
Hirose Y, Miura A, Kobayashi Y et al. · JID innovations : skin science from molecules to population health 2025 · PMID 40786655 · doi:10.1016/j.xjidi.2025.100394
This dataset
Open GSE273335 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 GSE273335_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 PRJNA1141442 and SRA study SRP522915. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40786655) ↗
Study design
12 conditions, mostly in triplicate
Skingraft, POD15, Non-Treatment, biological r… ×3 Skingraft, POD15, Non-Treatment, biological r… ×3 Skingraft, POD3, Non-Treatment, biological re… ×3 Skingraft, POD3, Non-Treatment, biological re… ×3 Skingraft, POD12, Non-Treatment, biological r… ×3 Skingraft, POD12, Non-Treatment, biological r… ×3 Skingraft, POD9, Non-Treatment, biological re… ×3 Skingraft, POD9, Non-Treatment, biological re… ×3 +4 more

Supports a between-group comparison across 34 samples.

How we read this: 12 replicated groups read from 34 sample titles; they account for 34 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
Datasets on a similar topic

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