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Collagen V regulates renal function after kidney injury and can be pharmacologically targeted to enhance kidney repair in mice [bulkRNAseq]

GSE290663 Mus musculus (mouse) RNA-seq (gene expression) 34 samples Submitted 2025/03/17 Platform GPL21103
At a glance

RNA-seq (gene expression) · mouse · 34 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
34 samples: 11 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
Collagen V regulates renal function after kidney injury and can be pharmacologically targeted to enhance kidney repair in miceScience translational medicine · 2025
Summary (written by the submitters)
Kidney fibrosis an important determinant of clinical outcomes in individuals with chronic kidney disease (CKD). The stoichiometric ratio of collagens in renal scar tissue differs from that of ECM of healthy kidneys but the functional importance of altered collagen types injured kidneys remains unclear. Using population studies and multiple independent clinical datasets, we show that circulating protein and renal mRNA amounts of Col5a1 exhibited associations with kidney disease and incident CKD risk.
Read the full summary ↓
Using murine models of tubulo-interstitial kidney injury, we show that Col V regulates the degree of post injury fibrosis and renal function. We demonstrated that mice with conditionally knocked out Col5a1 (Col5a1CKO ) exhibited decreased renal function and greater renal fibrosis after kidney injury . Renal fibroblasts in Col5a1CKO animals upregulated vβ3 integrin. Inhibition of vβ3 signaling with a small molecule, cilengitide, rescued post-injury renal function in Col5a1 CKO animals. Using the hybrid mouse diversity panel (HMDP) that comprises 100 diverse inbred strains of mice, we observed that the ratio of expression of Col5a1 after injury compared to healthy animals exhibited genetic variation . Strains with low Col5a1 ratios exhibited worse renal function compared to animals that had higher ratios . Col5a1 expression in peripheral blood mononuclear cells after injury compared to uninjured animals to identify Col5a1-non responder strains, we demonstrate that cilengitide can significan tly rescue kidney function in non-responder strains . Overall we found that Col V regulates renal function and fibrosis after kidney injury. These data suggest the feasibility of precision medicine approaches for targeting pathways downstream of Col5a1 to promote kidney repair.
Published in
Collagen V regulates renal function after kidney injury and can be pharmacologically targeted to enhance kidney repair in mice
Su L, Sun Q, Li Y et al. · Science translational medicine 2025 · PMID 40203084 · doi:10.1126/scitranslmed.ads7714
This dataset
Open GSE290663 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 GSE290663_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 PRJNA1229499 and SRA study SRP566781. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40203084) ↗
Study design
11 conditions, mostly in triplicate
AD28-CKO-Cilengitide ×4 ADE_14 ×3 ADE_28 ×3 ADE_7 ×3 NC ×3 AD28-CKO ×3 AD28-WT ×3 Co5a1-UUO_CT ×3 +3 more

Supports a between-group comparison across 34 samples.

How we read this: 11 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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