Exploring the utility of snRNA-seq in profiling human bladder tissue: A comprehensive comparison with scRNA-seq

Single cell sequencing technologies have revolutionized our understanding of biology by mapping cell diversity and gene expression in healthy and diseased tissues. While single-cell RNA sequencing (scRNA-seq) has been widely used, interest in single-nucleus RNA sequencing (snRNA-seq) is growing due to its benefits, including the ability to analyze archival tissues and capture rare cell types that are challenging to dissociate. However, comparative studies across tissues have yielded mixed results, with some reporting enhanced cell type retention using snRNA-seq while others finding cell type identification to be challenging in snRNA-seq data. The GUDMAP consortium aims to construct a molecular atlas of the lower urinary tract (LUT); thus, we set out to determine the strengths and limitations of each approach in characterizing LUT cell types. Using the human bladder, we determined that scRNA-seq offered more discriminative gene sets for identification while snRNA-seq could facilitate capture of previously underrepresented cell types. Eight healthy donor human bladder samples collected from the dome, neck, UO, and UVJ were subjected to RNA sequencing at either single cell or single nucleus resolution on Novaseq using 10X Gemonics library preparation platform. Data was processed using Cellranger v7.1.0 and anayzed using Seurat v4.3.0.1 to characterize various cell types and understand how single cell and single nucleus data contribute to each cell type's identification and gene set enrichment.