Extended Data Fig. 3: Kidney mesenchymal cells and proximal tubules.
From: Decoding myofibroblast origins in human kidney fibrosis
a, UMAP embedding of fibroblast, pericyte and myofibroblast cells from 13 human kidneys (n = 2,689). Colours represent the cell types. Lines refer to a lineage trajectory predicted by slingshot (Methods). b, Expression of selected genes on the embedding of a. c, Gene Ontology biological process analysis for pericyte, myofibroblast, fibroblast cell clusters and vascular smooth muscle cells based on the top marker genes for each cluster (CD10− data; see Methods). d, ECM score and scaled expression of select genes visualized on the mesenchymal cell diffusion map embedding of Fig. 1o. e–h, The distribution of ECM score, collagen score, glycoprotein score and proteoglycan scores stratified by epithelial cell clusters in the CD10− cell fraction. i, Scaled expression of select genes in proximal tubules and injured proximal tubule cell clusters. Each 100 cells are averaged in one column. j, GO biological process analysis based on differential expression between proximal tubules and injured proximal tubules. k–n, The distribution of ECM score, collagen score, glycoprotein score and proteoglycan scores for epithelial cells (CD10+ cell fraction). o, Percentage of cells expressing PDGFRβ and COL1α1 in each main cell niche. Neuronal Schwann cells were excluded because they are represented by a small number of cells.
