Fig. 3: scOpen characterizes the progression of kidney fibrosis.

a ARI values (y-axis) contrasting clustering results and transferred labels using distinct dimensional reduction methods for scATAC-seq. Clustering was performed by only considering UUO kidney cells on day 0 (WT), day 2, or day 10 or the integrated data set (all days). b UMAP of the integrated UUO scATAC-seq after doublet removal with major kidney cell types: fibroblasts, descending loop of Henle and thin ascending loop of Henle (DL & TAL); macrophages (Mac), Lymphoid (T and B cells), endothelial cells (EC), thick ascending loop of Henle (TAL), distal convoluted tubule (DCT), collecting duct-principal cells (CD-PC), intercalated cells (IC), podocytes (Pod) and proximal tubule cells (PT S1; PT S2; PT S3; Injured PT). c Proportion of cells of selected clusters on either day 0, day 2 or day 10 experiments. d Heatmap with TF activity score (z-transformed) for TFs (y-axis) and selected clusters (x-axis). We highlight TFs with the decrease in activity scores in injured PTs (Rxra and Hnf4a), with high TF activity scores in injured PTs (Batf:Jun; Smad2:Smad3) and immune cells (Creb1; Nfkb1). e Transcription factor footprints (average ATAC-seq around predicted binding sites) of Rxra, Smad2::Smad3 and Nfkb1 for selected cell types. The logo of underlying sequences is shown below and the number of binding sites is shown top-left corner. f Transcription factor footprints of Rxra, Smad2::Smad3, and Nfkb1 for injured PT cells in day 0, day 2, and day 10. Source data for Fig. 3 are provided as a Source Data file.