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Time‑course analysis of cisplatin induced AKI in preclinical models: implications for testing different sources of MSCs

GSE263678 Mus musculus (mouse) RNA-seq (gene expression) 32 samples Submitted 2024/05/31 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 32 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
32 samples: 8 conditions, mostly with about 4 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
Time-course analysis of cisplatin induced AKI in preclinical models: implications for testing different sources of MSCsJournal of translational medicine · 2024
Summary (written by the submitters)
Cisplatin remains the most effective and widely used treatment option for solid tumors, however, it is also responsible for 30 - 46% incidence of AKI in cancer patients. Thus, despite its broad anti-cancer potential, clinical use of this chemotherapeutic agent remains constrained. In the last decade, mesenchymal stem cells (MSCs) have been proposed as a potentially useful therapeutic strategy in various diseases, including AKI, given their ability to reduce apoptosis and accelerate tubular cell regeneration.
Read the full summary ↓
In the present study, we looked at the dose dependent response to cisplatin in two different mouse strains, CD1 and C57BL/6 mice, and performed a transcriptome based time-series analysis of the molecular signature in both male and female mice during progression of cisplatin-induced AKI, in order to generate a robust and reproducible pre-clinical model with the proposed aim to investigate the ability of MSCs from three different sources (adult and neonatal) as a rescue therapy to reverse kidney injury.
Published in
Time-course analysis of cisplatin induced AKI in preclinical models: implications for testing different sources of MSCs
Ganguly A, Chetty S, Primavera R et al. · Journal of translational medicine 2024 · PMID 39192240 · doi:10.1186/s12967-024-05439-6
This dataset
Open GSE263678 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 GSE263678_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 PRJNA1098743 and SRA study SRP500807. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39192240) ↗
Study design
8 conditions, mostly with about 4 replicates each
Day0_m ×4 Day0_f ×4 Day2_m ×4 Day2_f ×4 Day3_m ×4 Day3_f ×4 Day5_m ×4 Day5_f ×4

Supports a between-group comparison across 32 samples.

How we read this: 8 replicated groups read from 32 sample titles; they account for 32 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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