Spatial transcriptomic map of the mouse urinary bladder

We present a spatial transcriptomic map of the mouse urinary bladder at near single-cell resolution using Visium HD technology with 8 × 8 μm bins. After quality filtering, we analyzed 66,471 bins and 9,364 genes. Cluster annotation was supported by canonical marker genes and reference datasets, including Tabula Muris and Mouse Cell Atlas. Thirteen distinct clusters corresponding to major bladder compartments—the urothelium, lamina propria, and smooth muscle—were identified. Gene expression patterns revealed gradual transitions across tissue layers rather than sharp boundaries. Within the urothelium, basal, intermediate, and umbrella cells were distinguished, with umbrella cells showing potentially polarized mRNA distribution. The lamina propria primarily consisted of fibroblasts and a small number of immune cells. Four smooth muscle clusters were detected, contrasting with the single cluster typically identified by non-spatial single-cell RNA sequencing. This spatially resolved transcriptome map highlights the advantages of spatial transcriptomics in complementing traditional histology and scRNA-seq. Our map provides a valuable resource for advancing understanding of mouse urinary bladder biology and establishes a foundation for future studies of bladder pathology.