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Nephrotoxicity modelled ex vivo in the founder strains of the BXD mouse consortium

GSE334849 Mus musculus (mouse) RNA-seq (gene expression) 48 samples Submitted 2026/06/09 Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 48 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
48 samples: 16 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.
Summary (written by the submitters)
To investigate genetically determined susceptibility, we used precision-cut kidney slices (PCKS) from the two parental founder strains of the BXD mouse consortium, C57BL/6J and DBADBA/2J/2J. PCKS preserves tissue architecture and cell-cell interaction, allowing close experimental control while maintaining the renal microenvironment. Slices were exposed to cyclosporine A (80 nM for 6h, 20nM for 24h and 48h) and Tunicamycin (1 µM for 6h and for 24h) as well as normoxia (4°C for 20h) and hyperoxia (4°C for 20h and 4h in incubator).
Read the full summary ↓
Slices were then analysed using histopathological scoring, TUNEL staining, ATP quantification and bulk RNA sequencing. We found that the main source of variation was experimental duration. Nevertheless, a subtle difference between the strains could be observed for both cyclosporine A and Tunicamycin, with DBADBA/2J showing a stronger response to nephrotoxic stress, including lower ATP levels, higher proportion of apoptotic cells and a more pronounced transcriptomic response. For both strains, normoxia was the least harmful condition. These findings support the hypothesis that the BXD parental founder strains differ in their susceptibility to nephrotoxic kidney injury and support the use of PCKS as a relevant ex vivo model for studying early renal stress response. This provides the foundation to extend this approach to a broader spectrum of the BXD population to identify genetic loci and candidate genes involved in genetic susceptibility to nephrotoxins.
This dataset
Open GSE334849 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 GSE334849_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 PRJNA1476607 and SRA study SRP708076. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
16 conditions, mostly in triplicate
Male nephrotoxicity_control 6h_C57 ×3 Male nephrotoxicity_control 6h_DBA ×3 Male nephrotoxicity_Tunicamycin 6h_C57 ×3 Male nephrotoxicity_Tunicamycin 6h_DBA ×3 Male nephrotoxicity_Cyclosporin 6h_C57 ×3 Male nephrotoxicity_Cyclosporin 6h_DBA ×3 Male nephrotoxicity_control 24h_C57 ×3 Male nephrotoxicity_control 24h_DBA ×3 +8 more

Supports a between-group comparison across 48 samples.

How we read this: 16 replicated groups read from 48 sample titles; they account for 48 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

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

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