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Transcriptomic analysis of PM2.5 and/or fucoidan-treated ARPE-19 retinal pigment epithelial cells

GSE339345 Homo sapiens (human) RNA-seq (gene expression) 8 samples Submitted 2026/07/21 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 8 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
8 samples: 2 × ARPE-19 cells, vehicle control, vs 2 × ARPE-19 cells, fucoidan 400 micrograms/mL, vs 2 × ARPE-19 cells, PM2.5 200 micrograms/mL, vs 2 × ARPE-19 cells, PM2.5 plus fucoidan,Groups 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)
This study investigated the transcriptomic effects of PM2.5 in human ARPE-19 retinal pigment epithelial cells and evaluated the transcriptional responses associated with fucoidan treatment. ARPE-19 cells were assigned to four conditions: vehicle control, fucoidan (400 μg/mL), PM2.5 (200 μg/mL), and combined fucoidan plus PM2.5 treatment. Cells were treated for 24 hours before total RNA collection. RNA sequencing was performed to characterize PM2.5-induced gene expression changes and to determine how fucoidan modulates these transcriptional responses.
This dataset
Open GSE339345 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 GSE339345_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 PRJNA1498479 and SRA study SRP719911. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
2 × ARPE-19 cells, vehicle control, vs 2 × ARPE-19 cells, fucoidan 400 micrograms/mL, vs 2 × ARPE-19 cells, PM2.5 200 micrograms/mL, vs 2 × ARPE-19 cells, PM2.5 plus fucoidan,

Supports a between-group comparison across 8 samples.

How we read this: 4 replicated groups read from 8 sample titles; they account for 8 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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