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Impacts of Inorganic Arsenic Exposure on Genetic Stability of Human Mesenchymal Stromal Cells (hMSCs)

GSE293174 Homo sapiens (human) RNA-seq (gene expression) 38 samples Submitted 2025/07/09 Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 38 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
Homo sapiens (human)
Samples
38 samples: 10 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
Impacts of Inorganic Arsenic Exposure on Genetic Stability of Human Mesenchymal Stromal CellsJournal of applied toxicology : JAT · 2025
Summary (written by the submitters)
Human mesenchymal stem/stromal cells (hMSCs) can differentiate into mesoderm-type cells, making them suitable candidates for tissue repair therapies. However, their relatively low frequency in adult tissue necessitates ex vivo expansion prior to regenerative medicine applications. Expansion can lead to selection of chromosomally abnormal clones and therefore, long-term hMSC stability should be studied.
Read the full summary ↓
hMSCs applications in regenerative medicine ensures commercial availability of normal karyotype human primary cells for toxicity assessment and hMSCs could serve as alternatives to immortalized human cell models. In this work, we evaluated the potential of hMSCs in toxicity testing using inorganic arsenic (iAs) as a case study. hMSCs were exposed to iAs at different durations to track cellular aging and study long-term genetic stability. iAs exposures (48 hours) resulted in micronuclei induction. hMSCs were also exposed to iAs for 6 days to determine if hMSCs would become more susceptible to chromosomal damage following exposure to the model genotoxicant, mitomycin C (MMC). The culture duration and iAs exposure did not alter MMC potency, indicating that the hMSCs susceptibility to chromosomal damage remained unchanged. We also used gene expression analysis to investigate the molecular impacts of iAs on hMSCs over the course of short (3 days total) and long (30 days total) experiments. Both iAs exposures activated biomarkers associated with oxidative stress, but not biomarkers for direct DNA damage, providing support for an indirect mode of action for iAs genotoxicity. Overall, this study establishes the utility of hMSCs as a new model for toxicity screening and provides mechanistic information underlying iAs toxicity.
Published in
Impacts of Inorganic Arsenic Exposure on Genetic Stability of Human Mesenchymal Stromal Cells
Beal MA, Coughlan M, Nunnikhoven A et al. · Journal of applied toxicology : JAT 2025 · PMID 40241300 · doi:10.1002/jat.4785
This dataset
Open GSE293174 in finder → Find more human 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 GSE293174_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 PRJNA1243302 and SRA study SRP573860. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40241300) ↗
Study design
10 conditions, mostly with about 4 replicates each
hMSCs, untreated 3 days before experiment, Sa… ×4 hMSCs, vehicle 3 days culture, Sample ×4 hMSCs, 0.12uM 3 days culture, Sample ×4 hMSCs, 0.6uM 3 days culture, Sample ×4 hMSCs, 3uM 3 days culture, Sample ×4 hMSCs, vehicle 30 days culture, Sample ×4 hMSCs, 0.12uM 30 days culture, Sample ×4 hMSCs, 0.6uM 30 days culture, Sample ×4 +2 more

Supports a between-group comparison across 38 samples.

How we read this: 10 replicated groups read from 38 sample titles; they account for 38 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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