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New mechanisms for oral epithelial basal stem cell plasticity during re-epithelialization after injury

GSE281359 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2024/11/14 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 12 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
12 samples: 3 × wildtype mouse gingival tissue, injured, Day 3, biol vs 3 × wildtype mouse gingival tissue, non-injured control, Day 3, biol vs 3 × Irx1+/- heteozygote mouse gingival tissue, injured, Day 3, biol vs 3 × Irx1+/- heteozygote mouse gingival tissue, non-injured control, Day 3, biolGroups 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
Irx1 mechanisms for oral epithelial basal stem cell plasticity during reepithelialization after injuryJCI insight · 2025
Summary (written by the submitters)
The oral mucosa undergoes daily insults and stem cells in the epithelial basal cell layer are required to regenerate gingiva tissue to maintain oral health. The Iroquois Homeobox 1 (IRX1/Irx1) protein is expressed in the stem cell niches in human/mouse oral epithelium and mesenchyme under homeostasis. We found that Irx1+/- heterozygous (Het) mice have delayed wound closure, delayed morphological changes of regenerated epithelium, as well as defective keratinocyte proliferation and differentiation during wound healing.
Read the full summary ↓
RNA-seq analyses between wildtype and Irx1+/- mice at 3 days post injury (dpi), found impaired epithelial migration and decreased keratinocyte-related genes upon injury. Irx1 expressing cells are found in the gingival epithelial basal cell layer, a stem cell niche for gingival maintenance. Irx1 expressing cells are also found in cell niches in the underlying stroma. Irx1 activates Sox9 in the transient amplifying layer to increase cell proliferation and EGF signaling is activated to induce cell migration. Krt14CreERT lineage tracing experiments reveal defects in the stratification of the Irx1+/- heterozygous mouse oral epithelium. Irx1 is primed at the base of the gingiva in the basal cell layer of the oral epithelium, facilitating rapid and scarless wound healing through activating Sox9 and the EGF signaling pathway.
Published in
Irx1 mechanisms for oral epithelial basal stem cell plasticity during reepithelialization after injury
Su D, Krongbaramee T, Swearson S et al. · JCI insight 2025 · PMID 39782692 · doi:10.1172/jci.insight.179815
This dataset
Open GSE281359 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 GSE281359_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1183549 and SRA study SRP543909. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39782692) ↗
Study design
3 × wildtype mouse gingival tissue, injured, Day 3, biol vs 3 × wildtype mouse gingival tissue, non-injured control, Day 3, biol vs 3 × Irx1+/- heteozygote mouse gingival tissue, injured, Day 3, biol vs 3 × Irx1+/- heteozygote mouse gingival tissue, non-injured control, Day 3, biol

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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
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