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Modulating the Extracellular Matrix to Treat Wound Healing Defects in Ehlers-Danlos Syndrome

GSE264169 Mus musculus (mouse) RNA-seq (gene expression) 35 samples Submitted 2024/08/01 Platform GPL24247Platform GPL21493
At a glance

RNA-seq (gene expression) · mouse · 35 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
35 samples: 35 samples, each with a distinct title — no replicated groupsGroups 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
Modulating the extracellular matrix to treat wound healing defects in Ehlers-Danlos syndromeiScience · 2024
Summary (written by the submitters)
Classic Ehlers Danlos syndrome (cEDS) is one of the most common genetic disorders of the connective tissue and musculoskeletal system characterized by mutations in genes encoding for type V collagen. Defects in wound healing constitute one of the most common and debilitating symptoms in individuals with cEDS but currently, no therapeutic strategies exist to attenuate wound healing defects in cEDS.
Read the full summary ↓
We create a new murine model of cEDS, that remarkably phenocopies wound healing defects in human cEDS. Using this model, we show that an abnormal extracellular matrix (ECM) characterized by fibrillar disarray, altered mechanical properties and decreased collagen deposition contribute to the wound healing defect in cEDS. The cEDS animals exhibit decreased expression of epidermal genes and increased inflammation consistent with the human phenotype. We show that integrin expression is altered in wounds of cEDS animals and small molecule modulators of mechanosensitive integrin signaling attenuate wound healing defects. Finally, we demonstrate that rescuing extracellular matrix defects by injecting wild type fibroblasts into wounds of cEDS animals significantly enhances epidermal gene expression, decreases inflammation, augments wound closure and rescues defective wound repair. Taken together, these observations suggest that modulation of the extracellular matrix in Ehlers-Danlos syndrome either with small molecule inhibitors of mechanosensitive integrin signaling, or direct injection of wild type fibroblasts into the wound bed may have therapeutic potential for enhancing wound healing in cEDS.
Published in
Modulating the extracellular matrix to treat wound healing defects in Ehlers-Danlos syndrome
Kelly-Scumpia KM, Archang MM, Purbey PK et al. · iScience 2024 · PMID 39262784 · doi:10.1016/j.isci.2024.110676
This dataset
Open GSE264169 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 GSE264169_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 PRJNA1101088 and SRA study SRP502145. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39262784) ↗
Study design
35 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 35 sample titles: 35 distinct titles with little repetition. 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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