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Reprogramming of epidermal keratinocytes by PITX1 transforms the cutaneous cellular landscape and promotes wound healing [scRNA-seq]

GSE280067 Mus musculus (mouse) Single-cell RNA-seq 36 samples Submitted 2024/11/22 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 36 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Mus musculus (mouse)
Samples
36 samples: 10 conditions, mostly with about 4 replicates eachGroups 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
Reprogramming of epidermal keratinocytes by PITX1 transforms the cutaneous cellular landscape and promotes wound healingJCI insight · 2024
Summary (written by the submitters)
Skin injuries heal slowly, compared to oral epithelial tissues, and often do not regenerate lost adnexa. Using a murine mouse model expressing the oral epithelial transcription factor PITX1 in the skin, we performed scRNA-seq in healthy and wounded skin and healthy oral mucosa to delineate the cellular and molecular changes underpinning the superior oral wounding response.
Published in
Reprogramming of epidermal keratinocytes by PITX1 transforms the cutaneous cellular landscape and promotes wound healing
Overmiller AM, Uchiyama A, Hope ED et al. · JCI insight 2024 · PMID 39480496 · doi:10.1172/jci.insight.182844
This dataset
Open GSE280067 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 GSE280067_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 PRJNA1176133 and SRA study SRP540214. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39480496) ↗
Study design
10 conditions, mostly with about 4 replicates each
Day 0 Unwounded Skin Female Control ×5 Buccal Mucosa Unwounded Female Control ×4 Day 0 Unwounded Skin Female PITX1+ ×4 Day 0 Unwounded Skin Male PITX1+ ×4 Day 4 Post-Wounding Skin Female Control ×4 Day 4 Post-Wounding Skin Female PITX1+ ×4 Buccal Mucosa Unwounded Male Control ×3 Day 0 Unwounded Skin Male Control ×3 +2 more

Supports a between-group comparison across 36 samples.

How we read this: 10 replicated groups read from 36 sample titles; they account for 36 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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