Fig. 3.

Cell type composition in kidney of mouse CKD models and rat. a Cluster dendrogram showing similarity between 13 cell types that were confidently characterized in Park et al. Abbreviations: Neutro: neutrophils, Podo: podocytes, Endo: endothelials, LOH: loop of Henle, DCT: distal convolved tubule, PT: proximal tubule, CD-PT: collecting duct principal cell, CD-IC: CD intercalated cell, Macro: macrophages, Fib: fibroblasts, NK: natural killers. b–d Average estimated proportions for 6 cell types in bulk RNA-seq samples taken from three different studies, each study based on a different mouse model for chronic kidney disease. Results from three different deconvolution methods (MuSiC, BSEQ-sc and CIBERSORT) are shown by different colors. Supplementary Figure 5a–c show complete estimation results of all 13 cell types. b Bulk samples are from Beckerman et al., who sequenced 6 control and 4 APOL1 mice. c Bulk data are from Craciun et al.⁹, where samples are taken before (C) and at 1, 2, 3, 7, 14 days after administering folic acid. Line plot shows cell type proportion changes over time (days), averaged over 3 replicates at each time point. d Bulk data are from Arvaniti et al.¹⁰, where samples are taken from mice after Sham operation (C), 2 days after UUO operation (D2), and 8 days after UUO operation (D8). The average proportions at each time point are plotted. e MuSiC estimated cell type proportions of rat renal tubule segments. The estimated cell type proportions (left) and the proportions correlations between samples (right) are shown as heatmap. Segment names are color coded and aligned according to their physical positions along the renal tubule. Supplementary Figure 6a–c show NNLS, BSEQ-sc and CIBERSORT results. Segment name abbreviation: S1 S1 proximal tubule, S2 S2 proximal tubule, S3 S3 proximal tubule, SDL short descending limb, LDLOM long descending limb, outer medulla, LDLIM long descending limb, inner medulla, tAL thin ascending limb, mTAL medullary thick ascending limb, cTAL cortical thick ascending limb, DCT distal convoluted tubule, CNT connecting tubule, CCD cortical collecting duct, OMCD outer medullary collecting duct, IMCD inner medullar collecting duct. Source data are provided as a Source Data file