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Next Generation Sequencing facilitates to identify the differential expression genes of sorted conventional CD8+ T cells and MAIT cells

GSE223075 Homo sapiens (human) RNA-seq (gene expression) 35 samples Submitted 2025/03/21 Platform GPL16791
At a glance

RNA-seq (gene expression) · human · 35 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
35 samples: 10 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
Liver transplant-facilitated CD161(+)Vα7.2(+) MAIT cell recovery demonstrates clinical benefits in hepatic failure patientsNature communications · 2025
Summary (written by the submitters)
We obtained conventional CD8+T cells and MAIT cells 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. Based on the comparison results，we performed the GO and KEGG pathway enrichment analysis. That might suggest the different status of HBV-infected liver from liver surgery(AST<40) and liver transplantation(AST>40).
Published in
Liver transplant-facilitated CD161(+)Vα7.2(+) MAIT cell recovery demonstrates clinical benefits in hepatic failure patients
Wang W, Dai C, Zhu P et al. · Nature communications 2025 · PMID 40301342 · doi:10.1038/s41467-025-59308-x
This dataset
Open GSE223075 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 GSE223075_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 PRJNA924797 and SRA study SRP417912. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40301342) ↗
Study design
10 conditions, mostly in triplicate
cMAIT_HD, circulating MAIT cells from healthy… ×6 eMAIT_HD, expanded MAIT cells from healthy do… ×4 eMAIT_LT, expanded MAIT cells from HBV-relate… ×4 hMAIT_Comp, enriched hepatic MAIT cells from … ×4 cCD8+T_HD, circulating conventional CD8+T cel… ×3 cMAIT_LF, circulating MAIT cells from HBV-rel… ×3 eMAIT_LF, expanded MAIT cells from HBV-relate… ×3 hMAIT_LF, enriched hepatic MAIT cells from HB… ×3 +2 more

Supports a case/control comparison: 19 samples read as cases, 13 as controls.

How we read this: 10 replicated groups read from 35 sample titles; they account for 35 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.