Extended Data Fig. 1: Single cell phylogeny of kidney from an adult tissue snapshot.
From: Tracking single-cell evolution using clock-like chromatin accessibility loci
(a) UMAP projection of scATAC data of normal human kidney samples from biopsies. Abbreviations: LEUK: leukocytes; ENDO: endothelial cells; MES: mesangial cells; PEC: parietal epithelial cells; PODO: podocytes; PT: proximal tubule; PTPL: proximal tubule progenitor-like cell; LOH: loop-of-Henri; DCT: distal collection tubule; CD_PC: collection duct principal cell; CD_ICA: collection duct intercalating cell. (b) Single cell phylogeny built with chromatin accessibility on ClockDML (EpiTrace phylogeny). (c) Distribution of EpiTrace age for each cell type. Sample number of biologically independent cells: n = 845 (DCT1); 408 (DCT2); 484 (LOH); 537 (CD_ICA2); 404 (CD_ICA1); 437 (CD_PC1); 472 (CD_PC2); 111 (PEC); 80 (MES); 245 (ENDO); 234 (PODO); 60 (LEUK); 204 (PTPL); 544 (PT2); 881 (PT7); 901 (PT1); 486 (PT5); 763 (PT4); 1055 (PT6). (d) Cell age distribution of PT cells (colored by type) (top) and ATAC peak activity across cell age (bottom) in PT cells. Genes of interest are labelled on the right. Known translocation renal cell carcinoma (TRCC) driver gene: TFEB; known hereditary renal dysgenesis (CAKUT) genes: FGF8, FGFR2, SLIT3, GDNF, and NHS. For boxplots, the upper and lower bounds of boxes show 25% and 75% percentile of the data. The median of data is shown as horizontal line in the box. The distribution minima and maxima, defined as farthest datapoint distanced <= 1.5IQR from the box bounds, were shown by the whiskers. Violin plot shows the empirically estimated density distribution of data.
