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Effects of exposure to the trichloroethylene metabolite S-(1,2-dichlorovinyl)-L-cysteine on HTR-8/SVneo differential gene expression under hypoxic vs. normoxic conditions (O2 < 2%)

GSE287691 Homo sapiens (human) RNA-seq (gene expression) 16 samples Submitted 2025/01/24 Platform GPL34281
At a glance

RNA-seq (gene expression) · human · 16 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
16 samples: 4 × Hypoxia_10umDCVC_N vs 4 × Hypoxia_Control_N vs 4 × Normoxia_10umDCVC_N vs 4 × Normoxia_Control_NGroups 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
Exposure to the trichloroethylene metabolite S-(1,2-dichlorovinyl)-L-cysteine under hypoxic conditions (%O(2) =2 %) alters differential gene expression and mitigates decreased invasion capacity, compared to normoxic conditions (%O(2) ≥ 21 %) in HTR-8/SVneo cellsToxicology letters · 2025
Summary (written by the submitters)
Trichloroethylene (TCE) is an industrial solvent and widespread environmental contaminant. Human TCE exposure is prevalent, though epidemiological studies testing TCE exposure and adverse birth outcomes are inconclusive. The TCE metabolite S-(1,2-dichlorovinyl)-L-cysteine (DCVC) exhibits toxicity at human-relevant concentrations in a placental cell line.
Read the full summary ↓
To date, DCVC cytotoxicity mechanistic studies have only been performed under normoxic conditions. In the current study, two parallel experiments under hypoxic or normoxic conditions were conducted. Genome-wide gene expression and gene set enrichment analyses (GSEA) were used to identify novel genes and pathways altered by human exposure-relevant DCVC concentrations in the human placental cell line HTR-8/SVneo.
Published in
Exposure to the trichloroethylene metabolite S-(1,2-dichlorovinyl)-L-cysteine under hypoxic conditions (%O(2) =2 %) alters differential gene expression and mitigates decreased invasion capacity, compared to normoxic conditions (%O(2) ≥ 21 %) in HTR-8/SVneo cells
Stein FH, Le NH, Elkin ER · Toxicology letters 2025 · PMID 41232580 · doi:10.1016/j.toxlet.2025.111773
This dataset
Open GSE287691 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 GSE287691_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 PRJNA1214252 and SRA study SRP559073. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41232580) ↗
Study design
4 × Hypoxia_10umDCVC_N vs 4 × Hypoxia_Control_N vs 4 × Normoxia_10umDCVC_N vs 4 × Normoxia_Control_N

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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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