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Effects of dexamethasone and KLA on HepG2 gene expression

GSE278602 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/04/11 Platform GPL30173
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 × DMSO 0.1% (vehicle control), vs 3 × Dex 50nM, vs 3 × KLA 100ng/µl, vs 3 × Dex + KLA,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.
Paper
Activation of steroid hormone receptors by metabolism-disrupting chemicalsToxicology and applied pharmacology · 2025
Summary (written by the submitters)
In this study, we exposed HepG2 cells to synthetic glucocorticoid dexamethasone (Dex), Kdo2-Lipid A (KLA), or both (DexKLA) for 24 hours and conducted RNA-seq analysis to investigate the impact of exposures on gene expression. We aimed to elucidate how Dex and KLA disrupt, misregulate, or interfere with inflammatory and metabolic pathways at the transcriptional level. By analyzing the differential gene expression profiles, we sought to identify affected specific pathways and genes, providing insight into the underlying molecular mechanisms.
Published in
Activation of steroid hormone receptors by metabolism-disrupting chemicals
Pitkänen S, Niskanen J, Mysore R et al. · Toxicology and applied pharmacology 2025 · PMID 40216312 · doi:10.1016/j.taap.2025.117335
This dataset
Open GSE278602 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 GSE278602_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 PRJNA1168060 and SRA study SRP536194. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40216312) ↗
Study design
3 × DMSO 0.1% (vehicle control), vs 3 × Dex 50nM, vs 3 × KLA 100ng/µl, vs 3 × Dex + KLA,

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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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.