Extended Data Fig. 7: Spatial transcriptomic profiling of Col1α2-Ecm1+/+ and Col1α2-Ecm1-/- fibrotic kidneys.

(a, b) Spatial feature plots showing total transcript counts (nCount_Spatial) and detected gene features (nFeature_Spatial) in kidneys from Col1α2-Ecm1+/+ and Col1α2-Ecm1-/- mice (three biological pairs). (c) Clustering of the spots to reveal the spatial regions of kidney cortex and medulla. (d) Spatially resolved Ecm1 expression in Col1α2-Ecm1+/+ and Col1α2-Ecm1-/- kidneys. (e) Spatially resolved expression levels for fibrosis- and OXPHOS-related genes (Col1α1, Col1α2, Col3α1, Sdhb, Uqcrc1, Uqcrc2). (f) Violin plots showing normalized expression of Sdhb, Uqcrc1, Uqcrc2, and Slc34a1 between genotypes. (g) Spatially resolved expression of proximal tubular marker Slc34a1. (h) Deconvolution maps displaying spatial distribution of renal cell populations including distal convoluted tubule (DCT), endothelial cell (Endo), fibroblast (Fib), glomerular endothelial cell (GEC), intercalated cell (IC), immune cells (Immune), loop of Henle (LOH), podocyte (Podo), and proximal tubule (PT). (i) Dot plot summarizing marker gene expression across major renal cell types. (j) Spatial definition of fibrotic niches and their k nearest neighbors. For the violin plots, statistical significance was assessed using a two-sided Wilcoxon rank-sum test.