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the transcriptomic profiling of HCECs (PAI-2 knockout and control) exposed to PM2.5 for 3 hours

GSE290537 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/10/22 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 12 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
12 samples: 3 × HCECs, negative control, without treatment vs 3 × HCECs, negative control, with PM2.5 exposure for 3 hours vs 3 × HCECs, PAI-2 KO, without treatment vs 3 × HCECs, PAI-2 KO, with PM2.5 exposure for 3 hoursGroups 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
Corneal biomechanical cues mediated by PAI-2: the origin of PM2.5-induced corneal diseaseEMBO molecular medicine · 2026
Summary (written by the submitters)
We previously found that PAI-2 mediates long-term PM2.5 exposure-induced corneal damage in vivo and in vitro, while its role during subclinical stage remains unclear. In this study,we constructed PAI-2 knockout-human corneal epithelial cells (KO) and the negative control (NC). Transcriptome analysis was performed in three groups: NC, PM2.5-exposed NC, KO and PM2.5-exposed KO. These analysis suggested cell-ECM interactions might play an important role in PAI-2-induced corneal injury upon PM2.5 exposure.
Published in
Corneal biomechanical cues mediated by PAI-2: the origin of PM2.5-induced corneal disease
Hao S, Xie G, Li D et al. · EMBO molecular medicine 2026 · PMID 41326717 · doi:10.1038/s44321-025-00341-0
This dataset
Open GSE290537 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 GSE290537_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 PRJNA1228594 and SRA study SRP566481. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41326717) ↗
Study design
3 × HCECs, negative control, without treatment vs 3 × HCECs, negative control, with PM2.5 exposure for 3 hours vs 3 × HCECs, PAI-2 KO, without treatment vs 3 × HCECs, PAI-2 KO, with PM2.5 exposure for 3 hours

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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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