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Transcriptomic points of departure for 6PPD-Quinone derived from human Caco-2 and HepG2 cells

GSE302559 Homo sapiens (human) RNA-seq (gene expression) 72 samples Submitted 2025/08/15 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 72 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
72 samples: 18 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
Transcriptomic points of departure for 6PPD-Quinone derived from human Caco-2 and HepG2 cellsToxicology in vitro : an international journal published in association with BIBRA · 2025
Summary (written by the submitters)
N-(1,3-Dimethyl butyl)-N′-phenyl-phenylenediamine-quinone (6ppd-quinone) is of emerging concern due to its widespread presence and toxicity to aquatic species. The chemical has been detected in human biofluids though little is known about its effects on human tissues. The objective of this study was to increase understanding of 6ppd-quinone’s potential human health effects by deriving transcriptomic points of departure (tPOD) values in two human cell lines using the TPD-seq workflow.
Read the full summary ↓
An EC20 for cytotoxicity was calculated for Caco-2 (104µg/L) but not for HepG2 cells. Even in the absence of cytotoxicity, tPOD values (20th gene, 10th percentile, mode) were calculated in Caco-2 (6.5-25µg/L) and HepG2 (0.36-35µg/L) cells. These ranges capture values from 16 statistical and bioinformatic tests that examined mapping methods (CLC and Deplexer), algorithms (Limma and DESeq2), and filters (log2FC and BMR). The most common and sensitive genes with calculable benchmark doses (BMDs) in Caco-2 (DPF2, CD44, PGAP1, GDF15, H4C16) and HepG2 (SLC5A3, DKK1, ARG2, PHLDA1, TM4SF1) cells are listed. Pathway BMDs were also calculated for Caco-2 (systemic lupus erythematosus, 9.7-18µg/L; alcoholism, 9.7-20µg/L; viral carcinogenesis, 9.3-18.1µg/L), and HepG2 (metabolic pathways, 50-60µg/L) cells. These findings highlight TPD-seq as an efficient workflow to yield quantitative and mechanistic data relevant for human health risk assessment.
Published in
Transcriptomic points of departure for 6PPD-Quinone derived from human Caco-2 and HepG2 cells
Xu K, Mittal K, Basu N · Toxicology in vitro : an international journal published in association with BIBRA 2025 · PMID 40818648 · doi:10.1016/j.tiv.2025.106129
This dataset
Open GSE302559 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 GSE302559_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 PRJNA1291191 and SRA study SRP600805. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40818648) ↗
Study design
18 conditions, mostly in triplicate
Caco-2.control, ×12 HepG2.control, ×12 Caco-2.6ppdq.conc1, ×3 Caco-2.6ppdq.conc2, ×3 Caco-2.6ppdq.conc3, ×3 Caco-2.6ppdq.conc4, ×3 Caco-2.6ppdq.conc5, ×3 Caco-2.6ppdq.conc6, ×3 +10 more

Supports a between-group comparison across 72 samples.

How we read this: 18 replicated groups read from 72 sample titles; they account for 72 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

+ 32 more — browse all 72 samples with per-sample file links →

Datasets on a similar topic

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