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Assessing the Effects of Silver Nanoparticles on ARPE-19 Cells via High-Throughput Phenotypic Profiling with the Cell Painting Assay.

GSE297342 Homo sapiens (human) RNA-seq (gene expression) 88 samples Submitted 2025/05/20 Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 88 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
88 samples: 17 conditions, mostly with about 5 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
Assessing the effects of silver nanoparticles on ARPE-19 cells via high-throughput phenotypic profiling with the Cell Painting assayToxicology and applied pharmacology · 2025
Summary (written by the submitters)
Increasing commercialization of silver nanoparticles (AgNPs) has resulted in elevated opportunity for human exposure and outpaced traditional risk assessment approaches that rely on in vivo testing. Therefore, efficient methods are needed to evaluate potential hazards of AgNPs. Previous studies identified particle size and surface charge as determinants of AgNP toxicity, which has primarily been attributed to reactive oxygen species generation.
Read the full summary ↓
Those studies have generally focused on cytotoxicity or targeted cellular effects, potentially missing critical sub-cytotoxic effects. Here, high throughput phenotypic profiling (HTPP) with the Cell Painting assay was used to characterize the effects of 12 distinct AgNPs (≤ 30 µg/mL) on organelle morphology in human retinal pigmented epithelial cells (ARPE-19). Three coatings (branched polyethyleneimine, polyvinylpyrrolidone, citrate) were selected for their distinct surface charges and tested at 4 different sizes (40, 60, 80, 100 nm) to determine the effects of these properties on toxicity. HTPP was conducted in conjunction with a transcriptomic profiling experiment involving 60 nm particles of all coating types. This facilitated evaluation of mechanisms of action underlying morphological effects observed using HTPP. A cell viability and apoptosis assay was also run in parallel and used to exclude cytotoxic treatments from phenotypic and transcriptomic analyses. HTPP revealed concentration-dependent emergence of sub-cytotoxic phenotypic profiles that clustered by coating type, suggesting surface charge to be more influential than particle size in the determination of AgNP toxicity. The transcriptomic data highlighted oxidative stress and cell cycle alterations as fundamental underlying toxicity mechanisms of AgNPs.
Published in
Assessing the effects of silver nanoparticles on ARPE-19 cells via high-throughput phenotypic profiling with the Cell Painting assay
Byrd G, Goldstein-Plesser A, Nyffeler J et al. · Toxicology and applied pharmacology 2025 · PMID 40532858 · doi:10.1016/j.taap.2025.117444
This dataset
Open GSE297342 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 GSE297342_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 PRJNA1263555 and SRA study SRP585671. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40532858) ↗
Study design
17 conditions, mostly with about 5 replicates each
0.0 ug-Negative Control ×10 0.3 ug-AgCitrate ×7 1.0 ug-AgCitrate ×6 0.3 ug-AgBPEI ×5 0.3 ug-AgPVP ×5 1.0 ug-AgPVP ×5 10.0 ug-AgBPEI ×5 10.0 ug-AgCitrate ×5 +9 more

Supports a between-group comparison across 88 samples.

How we read this: 17 replicated groups read from 88 sample titles; they account for 88 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

+ 48 more — browse all 88 samples with per-sample file links →

Datasets on a similar topic

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