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scRNAseq analysis of cytokine-treated human islet cells

GSE251730 Homo sapiens (human) Single-cell RNA-seq 23 samples Submitted 2024/04/08 Platform GPL18573
At a glance

Single-cell RNA-seq · human · 23 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Homo sapiens (human)
Samples
23 samples: 8 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
Single Cell RNAseq Analysis of Cytokine-Treated Human Islets: Association of Cellular Stress with Impaired Cytokine ResponsivenessFunction (Oxford, England) · 2024
Summary (written by the submitters)
Pancreatic beta-cells are essential for survival, being the only cell type capable of insulin secretion. While they are believed to be vulnerable to damage by inflammatory cytokines such as interleukin-1 beta (IL-1beta) and IFN-gamma, we have recently identified physiological roles for cytokine signaling in rodent beta-cells that include that stimulation of antiviral and antimicrobial gene expression and the inhibition of viral replication.
Read the full summary ↓
In this study, we examine cytokine-stimulated changes in gene expression in human islets using single-cell RNA sequencing. Surprisingly, the global responses of human islets to cytokine exposure were remarkably blunted compared to our previous observations in the mouse. The small population of human islet cells that were cytokine responsive exhibited increased expression of IL-1beta-stimulated antiviral guanylate binding proteins, just like in the mouse. Most human islet cells were not responsive to cytokines, and this lack of responsiveness was associated with high expression of genes encoding ribosomal proteins. We further correlated the expression levels of RPL5 with stress response genes, and when expressed at high levels, RPL5 is predictive of failure to respond to cytokines in all endocrine cells. Further, we postulate that donor cause of death and isolation methodologies may contribute to stress of the islet preparation. Our findings indicate that induction of stress responses in human islets (associated with isolation and/or cause of death) limit cytokine stimulated gene expression, and we urge caution in the evaluation of studies that have examined cytokine-stimulated gene expression in human islets without evaluation of stress-related gene expression.
Published in
Single Cell RNAseq Analysis of Cytokine-Treated Human Islets: Association of Cellular Stress with Impaired Cytokine Responsiveness
Stancill JS, Kasmani MY, Cui W et al. · Function (Oxford, England) 2024 · PMID 38985000 · doi:10.1093/function/zqae015
This dataset
Open GSE251730 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 GSE251730_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1055142 and SRA study SRP479267. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38985000) ↗
Study design
8 conditions, mostly in triplicate
Human_islets_untreated ×3 Human_islets_6hr_IL-1b ×3 Human_islets_6hr_IFN-g ×3 Human_islets_6hr_IL-1b+IFN-g ×3 Human_islets_18hr_IL-1b+IFN-g ×3 Human_islets_18hr_IL-1b+IFN-g+NMMA ×3 Human_islets_18hr_NMMA ×3 Human_islets_18hr_IL-1b ×2

Supports a between-group comparison across 23 samples.

How we read this: 8 replicated groups read from 23 sample titles; they account for 23 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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