Fig. 3
Proximal tubule cell populations. a SWNE analysis of tubule clusters (3–14, 29) for cell types indicated (PT, DTL, ATL, TAL to DCT). Arrow indicates progression of lineages corresponding with expected spatial ordering in vivo. SWNE factor-associated genes (Supplementary Data 9) and relative medulla/cortex originations are indicated. b. Trajectory analysis of main PT clusters supporting their S1, S2 and S3 PT segment identities. c Heatmap of expression (row Z-scores) for genes differentially expressed along the proximal tubule trajectory (Supplementary Data 10) shown in (b). d Dot plot showing select segment-specific marker gene expression (averaged log scale values and percentage of expressed nuclei), localizing the PT clusters Unk and PT-4 to S2 and S3 segments. e Protein immunostaining (Human Protein Atlas49, Supplementary Data 16) for select PT markers, including general PT (LRP2), segment-specific (highlighted in c), and Unk/PT-4 cluster (CFH and FGA) markers. Arrows indicate representative protein localization. Scale bar indicates 25 µm. f UMAP plots as in Fig. 1b showing expression level (scaled from low—gray to high—blue) of S2 segment marker ACSM3 and Unk cluster 29 marker CFH. Lower panels show protein fluorescent immunostaining (Supplementary Data 17) for CFH in a subset of PT co-stained with AQP1 expression in PT, but not the PC marker AQP2 (arrows). Location of glomeruli (G) and scale bars (left panel—100 µm; right panel—50 µm) are indicated. Source data for (a−d, f) (UMAP plots) are provided as a Source Data file. UMAP uniform manifold approximation and projection, SWNE Similarity Weighted Nonnegative Embedding
