Exploring the utility of snRNA-seq in profiling human bladder tissue: A comprehensive comparison with scRNA-seq
Cite
Kim, J., Eo, E.Y., Kim, B., Lee, H., Kim, J., Koo, B.K., Kim, H.J., Cho, S., Kim, J. and Cho, Y.J., 2024. Transcriptomic Analysis of Air–Liquid Interface Culture in Human Lung Organoids Reveals Regulators of Epithelial Differentiation. Cells, 13(23), p.1991. https://doi.org/10.1016/j.isci.2024.111628
Abstract
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.
Datasets
Subject ID
Sample region
Cell type
Assay
Disease
Sex
Tissue
Ethnicity
Age
Bladder comaprtment
Sample ID
Leiden clustering
GEO accession
bladder_donor_629831 cells Ureterovesical Junction11498 cells Ureteral Orifice4672 cells Intermediate cells8108 cells Intra-muscular fibroblasts2899 cells General endothelial cells2485 cells General smooth muscle cells2028 cells Peri-urothelial fibroblasts1511 cells Lamina propria fibroblasts1105 cells CXCL14-hi fibroblast691 cells Venous endothelial cells484 cells Arterial endothelial cells446 cells Vascular smooth muscle cells398 cells Lymphatic endothelial cells225 cells Natural killer cells79 cells 10x 3' v3, single-nucleus7603 cells urinary bladder29831 cells Donor-6_UVJ-Nuc3310 cells Donor-6_Dome-Nuc1657 cells 2. Adult bladder urothelial subset
ExploreSubject ID
Sample region
Cell type
Assay
Disease
Sex
Tissue
Ethnicity
Age
Bladder comaprtment
Sample ID
GEO accession
Leiden clustering
bladder_donor_614776 cells Ureterovesical Junction5830 cells Ureteral Orifice563 cells Intermediate cells8108 cells 10x 3' v3, single-nucleus1497 cells urinary bladder14776 cells Donor-6_Dome-Nuc337 cells 3. Adult bladder stromal subset
ExploreSubject ID
Sample region
Cell type
Assay
Disease
Sex
Tissue
Ethnicity
Age
Bladder comaprtment
Sample ID
GEO accession
Leiden clustering
bladder_donor_612964 cells Ureterovesical Junction4633 cells Ureteral Orifice3907 cells Intra-muscular fibroblasts2899 cells General endothelial cells2485 cells General smooth muscle cells2028 cells Peri-urothelial fibroblasts1511 cells Lamina propria fibroblasts1105 cells CXCL14-hi fibroblast691 cells Venous endothelial cells484 cells Arterial endothelial cells446 cells Vascular smooth muscle cells398 cells Lymphatic endothelial cells225 cells 10x 3' v3, single-nucleus5737 cells urinary bladder12964 cells Donor-6_UVJ-Nuc2416 cells Donor-6_Dome-Nuc1190 cells 4. Adult bladder immune subset
ExploreSubject ID
Sample region
Cell type
Assay
Disease
Sex
Tissue
Ethnicity
Age
Bladder comaprtment
Sample ID
GEO accession
Leiden clustering
bladder_donor_62094 cells Ureterovesical Junction1038 cells Ureteral Orifice202 cells Natural killer cells79 cells 10x 3' v3, single-nucleus372 cells urinary bladder2094 cells Donor-6_Dome-Nuc130 cells 
