Extended Data Fig. 3: scRNA-seq and functional analysis of bladder assembloids.
From: Creation of bladder assembloids mimicking tissue regeneration and cancer
a, t-SNE plots of human cells (HULECs) in 1-day and 7-day bladder assembloids. b, Heat map representation of gene expression for the top 15 markers expressed in wild-type endothelial cell cluster A3 and A5 compared with human endothelial cell (HULECs) cluster of 1-day and 7-day bladder assembloids. Gene expression of HULECs in bladder assembloids are represented by orthologous genes (the list of orthologous genes is from ENSEMBL BioMart database). c, Split dot plot showing gene expression for the top 15 markers expressed in endothelial cell cluster A3 or A5 of wild-type bladder compared with endothelial clusters of 1-day or 7-day assembloid (circle size, proportion of cells; degree of shading, expression level). d, Comparative analysis between wild-type bladder and bladder assembloids for the proportions of individual cell types. e, Hierarchical clustering of distinct cell types shared by wild-type bladder, 1-day-old, and 7-day-old bladder assembloids using cell type-specific top 50 genes. f, Heat map representation of gene expression between clusters in four individual cell populations for top 15 markers expressed in wild-type bladder. g, Re-clustering of epithelial cell populations in 1-day and 7-day bladder assembloids from Fig. 2a identified five and four epithelial sub-clusters, respectively. h, The proportions of each cluster of 1-day and 7-day bladder assembloids shown in panel g. i, Violin plots for selected eight basal and luminal markers in each cell cluster shown in panel g. j, Bladder assembloids treated with acetylcholine (Ach) or noradrenaline (NA) were analysed using bright-field images and immunostaining. Scale bars, 100 μm. k, Transmission electron microcopy (TEM) and immunostaining analysis for tight junctions and urothelial plaques in bladder assembloids compared with wild-type bladder (black and white arrowheads, tight junctions; L, lumen; UP; urothelial plaques). Scale bars, 1 μm (TEM) or 10 μm (immunostaining). l, Immunostaining of ZO-1 for tight junctions in human bladder assembloids (white arrowheads, tight junctions; L, lumen). Scale bars, 20 μm. For details on statistics, sample sizes (n), and numbers of replications, see ‘Statistics and reproducibility’ (Methods).
