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To identify the differential expression of aGalcer/IL-2 treated T cells (iNKT) from human peripheral blood mononuclear cells of healthy donors (HD), chronic hepatitis B (CHB) and HBV-infected hepatocellular cacinoma (HCC) patients

GSE208038 Homo sapiens (human) RNA-seq (gene expression) 10 samples Submitted 2025/07/11 Platform GPL16791
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)
Topic
Hepatocellular carcinomaThis series is part of our curated briefing on it.
Samples
10 samples: 4 × HCC, peripheral blood, aGalcer/IL-2 treated, i'NKT cells, biol vs 3 × HD, aGalcer/IL-2 treated, i'NKT cells, biol vs 3 × CHB, peripheral blood, aGalcer/IL-2 treated, i'NKT cells, biolGroups 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.
Summary (written by the submitters)
To identify the different status of iNKT cells treated by aGalcer/IL-2 from CHB and HCC patients compared to HD. We enriched α-GalCer/IL-2 expanded iNKT cells from healthy donors (HD iNKT), CHB patients (CHB iNKT), and HBV-infected HCC patients (HCC iNKT) to rperforme next-generation sequencing (NGS). Illumina mRNA-seq sample preparation kit was used to perform paired-end library sequencing with Illumina HiSeq 2000 and sequence analysis was determined using the Illumina data analysis pipeline.
Read the full summary ↓
Based on the comparison results，we performed the GO and KEGG pathway enrichment analysis. That might suggest the different status of iNKT cells treated by aGalcer/IL-2 between HD, CHB and HBV-infected HCC patients.
This dataset
Open GSE208038 in finder → Find more human RNA-seq datasets → Hepatocellular carcinoma landscape →
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 GSE208038_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 PRJNA858049 and SRA study SRP386077. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
4 × HCC, peripheral blood, aGalcer/IL-2 treated, i'NKT cells, biol vs 3 × HD, aGalcer/IL-2 treated, i'NKT cells, biol vs 3 × CHB, peripheral blood, aGalcer/IL-2 treated, i'NKT cells, biol

Supports a between-group comparison across 10 samples.

How we read this: 3 replicated groups read from 10 sample titles; they account for 10 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
More Hepatocellular carcinoma datasets

Search all human RNA-seq datasets in GEO →

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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.