Extended Data Fig. 3: Cell type composition and analysis of glomerular regions.

a, Stacked bar plot showing the cell type proportions for individual glomerular regions across control and disease conditions. b, Boxplots showing comparisons of the cell type proportions in glomerular regions between control, SLE, ANCA-GN, and anti-GBM conditions. The number of datapoints (cells per disease) used to create boxplots are—Cntrl: 29,035, SLE: 47,266, ANCA: 61,708, GBM: 31,744. Boxplots show the median (middle horizontal line), interquartile range (box), Tukey-style whiskers (lines beyond the box), outliers (data points beyond 1.5*interquartile or below −1.5*interquartile). c, Heatmap showing Pearson correlation coefficients between different ROI cell types (glomerular and abundant immune cell types) based on their transcriptional profiles. The heatmap displays strong positive correlations between MCs and fibrotic MCs (r = 0.55). d, Dot plot showing expression patterns of immune, glomerular, and fibrosis-related genes across cell types. Dot sizes represent the fraction of cells within the ROIs expressing each gene, and dot colors indicate scaled mean expression levels. e, Heatmap displaying the mean expression of selected genes in MC and fibrotic MC populations, highlighting transcriptional differences between these cell states. f, Line plot showing the change in proportions of MCs and fibrotic MCs ordered by PC1. The inverse relationship demonstrates potential transition from MC to fibrotic MC phenotype along this axis. Pearson’s correlation coefficient (r) and associated two-sided p-value (1.97e-174).