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_629,831 cells Ureterovesical Junction11,498 cells Ureteral Orifice4,672 cells Intermediate cells8,108 cells Intra-muscular fibroblasts2,899 cells General endothelial cells2,485 cells General smooth muscle cells2,028 cells Peri-urothelial fibroblasts1,511 cells Umbrella cells1,489 cells Lamina propria fibroblasts1,105 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-nucleus7,603 cells urinary bladder29,831 cells Donor-6_UVJ-Nuc3,310 cells Donor-6_UO-Nuc1,669 cells Donor-6_Dome-Nuc1,657 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_614,776 cells Ureterovesical Junction5,830 cells Ureteral Orifice563 cells Intermediate cells8,108 cells Umbrella cells1,489 cells 10x 3' v3, single-nucleus1,497 cells urinary bladder14,776 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_612,964 cells Ureterovesical Junction4,633 cells Ureteral Orifice3,907 cells Intra-muscular fibroblasts2,899 cells General endothelial cells2,485 cells General smooth muscle cells2,028 cells Peri-urothelial fibroblasts1,511 cells Lamina propria fibroblasts1,105 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-nucleus5,737 cells urinary bladder12,964 cells Donor-6_UVJ-Nuc2,416 cells Donor-6_UO-Nuc1,386 cells Donor-6_Dome-Nuc1,190 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_62,094 cells Ureterovesical Junction1,038 cells Ureteral Orifice202 cells Natural killer cells79 cells 10x 3' v3, single-nucleus372 cells urinary bladder2,094 cells Donor-6_Dome-Nuc130 cells 
