Fig 1: scRNA-seq delineates distinct types of cells derived from Wnt4-expressing cells and the effects of Smarca4 deficiency in these cells. (A) Unsupervised clustering demonstrates 24 distinct cell types shown in a tSNE plot of Wnt4 Cre -labled cells of control and Smarca4 cKO/cKO . (B) Percentages of assigned cell types are summarized in the right panel. NP, nephron progenitor; SSB, S-shaped body; NPC, nephron progenitor cell; PT, proximal tubule; EPT, early PT, SMCs, smooth muscle cells; CD-associated stroma, collecting duct-associated stroma; (C) tSNE plots showing restricted Wnt4 expression. (D) Violin plot showing the expression levels of representative marker genes across the 24 main clusters. The y-axis shows the long-scale normalized read count. (E) tSNE plots showing Pdgfrα in stroma cells, Pecam1 expression in endothelial cells and Foxd1 expression in stroma of nephrogenic, cortical and podocytes. (F) Immunostaining for Foxd1, Pecam1, Tyrobp, Tnnt2 and SMA showing colocalization with tdTomato+ cells in Wnt4 Cre/+ ;R26-tdTomato kidneys (arrows). Scale bar: 60 μm.