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Hypothermic oxygenated machine perfusion influences the immunogenicity of donor livers in humans

GSE276531 Homo sapiens (human) RNA-seq (gene expression) 32 samples Submitted 2024/11/08 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 32 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
32 samples: 9 × DBD_cold_B.POST_A vs 9 × DBD_cold_B.PRE_A vs 7 × DBD_machine_B.POST_A vs 7 × DBD_machine_B.PRE_AGroups 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
Hypothermic oxygenated machine perfusion influences the immunogenicity of donor livers in humansLiver transplantation : official publication of the American Association for the Study of Liver Diseases and the International Liver Transplantation Society · 2025
Summary (written by the submitters)
Hypothermic oxygenated machine perfusion (HOPE) is an organ preservation strategy shown to reduce ischemia-reperfusion-injury (IRI)-related complications following liver transplantation this remains to be evaluated in humans. Analysis of liver tissue transcriptome at reperfusion revealed an effect of HOPE on the reactive oxygen species pathway.
Read the full summary ↓
Two weeks post transplantation, HOPE recipients exhibited increased circulating CD4+FOXP3+CD127lo regulatory T cells (Tregs) (p<0.01), which corresponded to a higher frequency of donor specific Tregs (p<0.01) and was followed by reduced alloreactivity index of CD8+ T cells 3 months post-transplant. Our study provides novel mechanistic insight into the capacity of HOPE to influence liver IRI and to modulate effector and regulatory donor-specific Tcell responses post-transplantation. These findings, which confirm observations made in animal models, help explain the decreased rejection rates reported in patients receiving HOPE-treated allografts.
Published in
Hypothermic oxygenated machine perfusion influences the immunogenicity of donor livers in humans
Elgosbi M, Kurt AS, Londoño MC et al. · Liver transplantation : official publication of the American Association for the Study of Liver Diseases and the International Liver Transplantation Society 2025 · PMID 39172015 · doi:10.1097/LVT.0000000000000461
This dataset
Open GSE276531 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 GSE276531_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 PRJNA1157785 and SRA study SRP531055. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39172015) ↗
Study design
9 × DBD_cold_B.POST_A vs 9 × DBD_cold_B.PRE_A vs 7 × DBD_machine_B.POST_A vs 7 × DBD_machine_B.PRE_A

Supports a between-group comparison across 32 samples.

How we read this: 4 replicated groups read from 32 sample titles; they account for 32 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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