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Isolation and characterization of an islet-associated CD45- MHC class II+ cells using single cell RNA sequencing.

GSE292898 Homo sapiens (human) Single-cell RNA-seq 11 samples Submitted 2025/12/02 Platform GPL30172Platform GPL30173
At a glance

Single-cell RNA-seq · human · 11 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
11 samples: 11 samples, each with a distinct title — no replicated groupsGroups 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
A vascular-associated fibroblastic cell controls pancreatic islet immunityCell reports · 2025
Summary (written by the submitters)
MHC-II is expressed in normal murine and human islets by cells that are located at the periphery of the islet and associated with the efferent vasculature. These cells are non-hematopoietic in origin based on their non-expression of CD45, and split in two families, vascular and fibroblastic, based on their gene transcription profiles, their morphology, and their location.
Published in
A vascular-associated fibroblastic cell controls pancreatic islet immunity
Clarke D, Costanzo A, Sharma S et al. · Cell reports 2025 · PMID 40884792 · doi:10.1016/j.celrep.2025.116189
This dataset
Open GSE292898 in finder → Find more 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 GSE292898_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 PRJNA1241824 and SRA study SRP573009. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40884792) ↗
Study design
11 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 11 sample titles: 11 distinct titles with little repetition. 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.