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Gene expression profiling of tunicamycin-induced ER stress in HepG2 hepatoma cells

GSE296996 Homo sapiens (human) RNA-seq (gene expression) 10 samples Submitted 2025/12/10 Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 10 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
10 samples
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
AP-1 elements in the promoter and second intron mediate endoplasmic reticulum stress-induced expression of the GPAT3 geneScientific reports · 2025
Summary (written by the submitters)
Endoplasmic reticulum (ER) stress, a disruption of ER homeostasis, is involved in the pathophysiology of several human diseases, including metabolic dysfunction-associated steatotic liver disease (MASLD). MASLD, formerly known as nonalcoholic fatty liver disease (NAFLD), is characterized by an excessive accumulation of hepatic lipids.
Read the full summary ↓
To characterize ER stress-induced changes in the expression of genes involved in lipid metabolism, HepG2 human hepatoma cells were exposed to tunicamycin, followed by transcriptome profiling. Among genes involved in lipid biosynthesis, GPAT3 was strongly activated by tunicamycin while many other genes involved in this process (e.g., DGAT2, AGPAT2, AGPAT3, GPAT1, DGAT1 and GPAT4) were downregulated. Since GPAT proteins catalyze rate-limiting step in the de novo synthesis of glycerophospholipids and triglycerides, the unique expression pattern of GPAT3 potentially links it to ER stress-associated accumulation of lipids in hepatic cells.
Published in
AP-1 elements in the promoter and second intron mediate endoplasmic reticulum stress-induced expression of the GPAT3 gene
Örd D, Örd T, Gluboki E et al. · Scientific reports 2025 · PMID 41392190 · doi:10.1038/s41598-025-32503-y
This dataset
Open GSE296996 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 GSE296996_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 PRJNA1262349 and SRA study SRP584854. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41392190) ↗
Samples in this study

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