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Decoding the molecular complexity governing corneal wound closure in vivo

GSE292450 Mus musculus (mouse) RNA-seq (gene expression) 60 samples Submitted 2025/04/04 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 60 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
60 samples: 12 conditions, mostly with about 5 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
Decoding epithelial regeneration in the cornea: multi-omic analysis reveals cellular plasticity as central mechanismCellular & molecular biology letters · 2025
Summary (written by the submitters)
The cornea, the transparent outermost layer of the eye, possesses exceptional wound healing capabilities essential for vision preservation. The complexity of the corneal microenvironment is central to its rapid healing; however, the molecular mechanisms orchestrating this process remain poorly defined, limiting therapeutic advancements.
Read the full summary ↓
Here, we elucidate the extensive remodeling of the corneal molecular landscape following physical injury. Multi-omics analyses—including transcriptomic, epitranscriptomic, and proteomic profiling—uncover significant induction of epithelial cell plasticity driving wound closure. Moreover, lacrimal gland ablation further suppresses Pax6 expression, highlighting its regulatory role. Our multi-omic approach uniquely reveals bilateral remodeling of the molecular environment, a phenomenon constrained by an intact tear film. Collectively, our findings identify novel molecular factors critical to corneal healing, significantly advancing the understanding of epithelial plasticity. These insights will facilitate the translation of cell plasticity research into innovative strategies for tissue and organ regeneration.
Published in
Decoding epithelial regeneration in the cornea: multi-omic analysis reveals cellular plasticity as central mechanism
Feret N, Megido AC, Kuony A et al. · Cellular & molecular biology letters 2025 · PMID 41177882 · doi:10.1186/s11658-025-00804-9
This dataset
Open GSE292450 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 GSE292450_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 PRJNA1238787 and SRA study SRP571874. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41177882) ↗
Study design
12 conditions, mostly with about 5 replicates each
Murine cornea, 3 months, 6 hours post-abrasio… ×5 Murine cornea, 3 months, 6 hours post-abrasio… ×5 Murine cornea, 3 months, 12 hours post-abrasi… ×5 Murine cornea, 3 months, 12 hours post-abrasi… ×5 Murine cornea, 3 months, 18 hours post-abrasi… ×5 Murine cornea, 3 months, 18 hours post-abrasi… ×5 Murine cornea, 3 months, 24 hours post-abrasi… ×5 Murine cornea, 3 months, 24 hours post-abrasi… ×5 +4 more

Supports a between-group comparison across 60 samples.

How we read this: 12 replicated groups read from 60 sample titles; they account for 60 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

+ 20 more — browse all 60 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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