Extended Data Fig. 2: Expression of cell type markers and ECM score.
From: Decoding myofibroblast origins in human kidney fibrosis
a, Scaled gene expression of marker genes in mesenchymal cell clusters of the CD10− data depicted in Fig. 1b–e. Each 100 cells are averaged in one column. b, As in a, but endothelial clusters. c, As in a, but immune clusters. d, As in a but epithelial clusters. e, The seven cell clusters found in the CD10+ fraction cells visualized on the UMAP embedding from Fig. 1e. f, UMAP embedding of e with colours representing the cell types/states. g, Scaled ECM score on UMAP from e. h, Eight patients visualized on UMAP embedding as in e. i, Expression of RBP4 visualized on UMAP embedding from e. j, Scaled gene expression of the top 20 genes by specificity of each of the 7 cell clusters discovered in the CD10+ data depicted in e–h. k, log-transformed fold change of cell cycle stage assignment frequencies in healthy and CKD epithelial cells relative to permuted frequencies. Positive numbers represent enrichment; negative numbers represent depletion. l, Percentage of cells per cell cluster in each cell cycle phase as predicted from gene expression data. m, n, KEGG and GEO process terms enriched in cells belonging to healthy controls or patients with CKD, according to differentially expressed genes between healthy and diseased patients (see Fig. 1f). Note fatty acid catabolic process and lipid oxidation consistent with KEGG pathway enrichment results o, ECM, collagen, proteoglycan and glycoprotein score of human diabetic kidney dataset8. Advanced diabetic nephropathy (DN) n = 21, early DN n = 6, control n = 9. p, Distribution of single-cell ECM scores for all cells in the CD10− cell fraction, colours indicate cell groups obtained by unsupervised mixture model clustering of ECM scores. q, ECM groups visualized on the UMAP of Fig. 1b. r, ECM scores as in p, but scaled and visualized on the UMAP embedding from Fig. 1b. s–u, Scaled expression of gene groups summarized in the ECM score including collagens (r), glycoproteins (s) and proteoglycans (t). All 50 cell clusters are shown, all cells from each cluster are averaged in one column.
