Evaluating cell-specific gene expression using single-cell and single-nuclei RNA-sequencing data from human pancreatic islets of the same donors.

ABSTRACT: Single-cell and single-nuclei RNA-sequencing (scRNA-seq and snRNA-seq) analyze cell-specific transcriptomes. However, only snRNA-seq applies to frozen biobanked samples. For human pancreatic islets, marker genes and reference-based cell type annotation methods are mainly from scRNA-seq datasets and may not be suitable for snRNA-seq. We compared human islet scRNA-seq and snRNA-seq data from the same donors (N = 4) and evaluated annotation methods by studying cell type composition and gene detection, and identified novel marker genes. We compared cell type annotations: (1) manual annotation based on identified marker genes, (2) reference-based annotation using Azimuth's scRNA-seq pancreasref dataset, or (3) Seurat's label transfer from the Human Pancreas Analysis Program (HPAP) scRNA-seq dat

SUBMITTER: Engstrom K 

PROVIDER: S-EPMC12533216 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature