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Uncovering shared Molecular and Histopathological features of accepted versus rejected donor livers for transplantation

GSE243887 Homo sapiens (human) RNA-seq (gene expression) 32 samples Submitted 2024/04/18 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: 32 × Donor liver biopsyGroups 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
Integrated transcriptomics and histopathology approach identifies a subset of rejected donor livers with potential suitability for transplantationBMC genomics · 2024
Summary (written by the submitters)
Liver transplantation is the solution for acute or chronic liver failure. There is an unmet demand for liver transplantation, as not all donated organs are transplanted. The clinical selection criteria for donated livers depends on histopathological evaluation and liver function tests. A fraction of the donor livers are rejected for transplantation due to the variability in applying the selection criteria.
Read the full summary ↓
We applied an integrated transcriptomics and histopathological approach to characterize the donor livers evaluated for transplantation. We obtained liver biopsies from deceased donors during organ collection (n=10 accepted and n= 21 rejected for transplantation). We performed RNA sequencing to characterize the global gene expression profiles. We assessed steatosis, fibrosis, and necrosis via manual histopathological evaluation and a custom artificial intelligence-based image analysis. We identified two transcriptomically distinct subsets in the rejected donor liver group (termed rejected-1 and rejected-2), where the rejected-2 subset had a near complete transcriptomic overlap with the accepted livers, suggesting the potential for acceptability from a molecular standpoint. The liver metabolic functional genes were similarly upregulated in the accepted and rejected-2 groups compared to the rejected-1 subset. Expression levels of several extracellular matrix genes were similarly low in the accepted and rejected-2 groups compared to the rejected-1 subset. Filtering the rejected-2 subset based on histopathological evaluation identified the cases with borderline scores and extensive molecular overlap with the accepted group. Our integrated molecular and histopathological approach identified a subset of rejected donor livers that may be suitable for transplantation, thereby expanding the pool of transplantable livers.
Published in
Integrated transcriptomics and histopathology approach identifies a subset of rejected donor livers with potential suitability for transplantation
Srivastava A, Manchel A, Waters J et al. · BMC genomics 2024 · PMID 38698335 · doi:10.1186/s12864-024-10362-7
This dataset
Open GSE243887 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 GSE243887_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 PRJNA1020411 and SRA study SRP462846. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38698335) ↗
Study design
32 × Donor liver biopsy

Supports a between-group comparison across 32 samples.

How we read this: 1 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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