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Comparative analysis of gene expression upon IFNα stimulation in hepatocyte-like cells [IFN]

GSE288203 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/04/23 Platform GPL20301
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 × dHepaRG_IFN vs 3 × dHepaRG_Mock vs 3 × dHuh7.5-NTCP_IFN vs 3 × dHuh7.5-NTCP_MockGroups 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
A novel in vitro system for simultaneous infections with hepatitis B, C, D and E virusesJHEP reports : innovation in hepatology · 2025
Summary (written by the submitters)
Patients chronically co-infected by Hepatitis B Virus (HBV) and Hepatitis D Virus (HDV) suffer from the most aggressive form of viral hepatitis leading to severe liver disease such as cirrhosis, hepatocellular carcinoma and liver decompensation. Treatments options are very limited with only two drugs used in clinic (IFN-α and Bulevertide) that rarely allow viral clearance.
Read the full summary ↓
The molecular mechanisms leading to inhibition of HDV by IFN-α (in patients but also in vitro) are not known and mechanisms behind treatment failures in patients also remain elusive. Here we aimed at the identification of interferon stimulated genes (ISGs) that can specifically inhibit intracellular HDV replication. IFN-α was able to inhibit HDV in both co-infected differentiated HuH7.5-NTCP- and HepaRG cells (dHuH7.5-NTCP and dHepaRG, respectively). We hypothesized that ISGs responsible for the antiviral effect of HDV should be upregulated in both dHepaRG and dHuH7.5-NTCP cells upon treatment with IFN-α. To identify these ISGs, dHuh7.5-NTCP and dHepaRG cells were stimulated with IFN-α for 8h, total RNAs were extracted and gene expression was analyzed by RNAseq.
Published in
A novel in vitro system for simultaneous infections with hepatitis B, C, D and E viruses
Fouillé R, Verrier ER, De Meyer A et al. · JHEP reports : innovation in hepatology 2025 · PMID 40242313 · doi:10.1016/j.jhepr.2025.101383
This dataset
Open GSE288203 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 GSE288203_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 PRJNA1216564 and SRA study SRP560367. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40242313) ↗
Study design
3 × dHepaRG_IFN vs 3 × dHepaRG_Mock vs 3 × dHuh7.5-NTCP_IFN vs 3 × dHuh7.5-NTCP_Mock

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
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