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Transcriptomic Changes in Human Pulmonary Fibroblasts Following Microplastics Exposure

GSE296007 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2025/06/30 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 24 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
24 samples: 8 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.
Paper
Tracing micro and nanoplastics toxicity in human pulmonary fibroblasts through integrated Raman and transcriptomic analysesScientific reports · 2025
Summary (written by the submitters)
To assess the cellular effects of polystyrene (PS) micro- and nanoparticles, human pulmonary fibroblasts (HPFs) were exposed to spherical PS particles of two diameters (100 nm and 1 µm) across multiple concentrations. For 100 nm particles, the concentrations were 0.1 g/L (A), 0.01 g/L (B), and 0.001 g/L (C); for 1 µm particles, 0.1 g/L (A), 0.05 g/L (D), 0.01 g/L (B), and 0.001 g/L (C) were tested.
Read the full summary ↓
In summary, our data show that both particle size and concentration critically influence the cellular response to microplastics. At low concentrations (0.001 g/L), smaller particles (100 nm) induced transcriptional activation of mitochondrial and biosynthetic genes, suggesting early metabolic adaptation. In contrast, high concentrations (0.1 g/L), particularly of larger particles (1 µm), led to suppression of metabolic, mitochondrial, and proteostatic pathways, indicating functional impairment and potential cellular stress.
Published in
Tracing micro and nanoplastics toxicity in human pulmonary fibroblasts through integrated Raman and transcriptomic analyses
Chwiej J, Wytrwal M, Papacz K et al. · Scientific reports 2025 · PMID 41219303 · doi:10.1038/s41598-025-22947-7
This dataset
Open GSE296007 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 GSE296007_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 PRJNA1257307 and SRA study SRP582372. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41219303) ↗
Study design
8 conditions, mostly in triplicate
Pulmonary cells, control, ×3 Pulmonary cells, Microplastics 1um, 0.1 g/L (… ×3 Pulmonary cells, Microplastics 1um, 0.05 g/L … ×3 Pulmonary cells, Microplastics 1um, 0.01 g/L … ×3 Pulmonary cells, Microplastics 1 um, 0.001 g/… ×3 Pulmonary cells, Nanoplastics 100 nm, 0.1 g/… ×3 Pulmonary cells, Nanoplastics 100 nm, 0.01 g/… ×3 Pulmonary cells, Nanoplastics 100 nm, 0.001 g… ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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
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