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Cross-Species Comparison between Mouse Kidney Multi-Omics and Human Genome-Wide Association Studies Highlights Molecular Features Associated with Oxalate Nephropathy

GSE282711 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/04/30 Platform GPL19057
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: 4 × B57BL/6, kidney, control (no treatment), sample numbe vs 4 × B57BL/6, kidney, glyoxylate-treated mice for day1, sample numbe vs 4 × B57BL/6, kidney, glyoxylate-treated mice for day6, sample numbeGroups 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
Cross-Species Comparison between Mouse Kidney Multi-Omics and Human Genome-Wide Association Studies Highlights Molecular Features Associated with Oxalate NephropathyKidney360 · 2026
Summary (written by the submitters)
Urolithiasis, a recurrent and increasingly prevalent disease globally, has a complex pathophysiology that impedes comprehensive understanding. This study sought to identify new pathogenetic molecules linked to urolithiasis through multi-omics analysis of a urolithiasis mouse model's kidneys and human genome-wide association analysis (GWAS).
Read the full summary ↓
In the multi-omics analysis of urolithiasis mouse kidneys using RNA-seq, whole cell proteome, and phosphoproteome, we identified 1,173 genes, 342 proteins, and 516 phosphorylated peptides which were differentially expressed (DE) when comparing model with control mice. We employed large-scale urolithiasis GWAS resources from BioBank Japan, UK Biobank, and FinnGen through a meta-analysis, which provided 343 urolithiasis-related genes by gene enrichment analysis. Integrating the results of mouse and human analyses, we identified 46 urolithiasis-associated candidate molecules shared across species. We then further validated relevance of these 46 molecules in human urolithiasis. DE analysis comparing gene expression of the human renal papilla with and without stones found upregulation of CRYAB and SHROOM3, which are specifically expressed in collecting duct principal cells. Colocalization analysis between urolithiasis GWAS and expression quantitative trait loci (eQTL) data of human renal tubules revealed colocalization for GLUD1, UMOD, SLC34A1, and TCEA3. Colocalization analysis between the urolithiasis GWAS and 51 urolithiasis-related human phenotype GWAS found that SNX17 and UMOD showed prominent genetic pleiotropy. This study not only highlights novel urolithiasis-related molecules such as CRYAB, SHROOM3, TCEA3, and SNX17 but also elucidates cell types harboring the effects of known urolithiasis-related molecules. Consequently, successful mapping of renal effectuating molecules in urolithiasis has been achieved.
Published in
Cross-Species Comparison between Mouse Kidney Multi-Omics and Human Genome-Wide Association Studies Highlights Molecular Features Associated with Oxalate Nephropathy
Chaya R, Taguchi K, Hashimoto Y et al. · Kidney360 2026 · PMID 42275142 · doi:10.34067/KID.0000001211
This dataset
Open GSE282711 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 GSE282711_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 PRJNA1189835 and SRA study SRP547177. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42275142) ↗
Study design
4 × B57BL/6, kidney, control (no treatment), sample numbe vs 4 × B57BL/6, kidney, glyoxylate-treated mice for day1, sample numbe vs 4 × B57BL/6, kidney, glyoxylate-treated mice for day6, sample numbe

Supports a case/control comparison: 8 samples read as cases, 4 as controls.

How we read this: 3 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
Datasets on a similar topic

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