Extended Data Fig. 5: Supporting information for clonal lineage tracing across accessible chromatin landscapes and time in an in vitro model of hematopoiesis.

(a) Depiction of single-cell UMAP embedding showing the original distribution of cells for each library/ time point, (b) relative cell density, (c) Louvain cluster, and (d) mitochondrial DNA coverage per single cell. (e) Overlap of variants called for each of the two datasets. (f) Comparison of log2 fold change in heteroplasmy from day 14 to day 8 for 19 overlapping variants. The p-value shown is for the beta 1 coefficient of the depicted linear regression model. (g) Proportion of cells (%) at day 8 of the 500 cell (x axis) and 800 cell (y axis) input culture carrying shared mtDNA variants as derived from panel (e) suggests limited clonal overlap. (h) Known pathogenic mtDNA mutations detected from a healthy donor. Each dot is a cell separated by the sampled library. All cells with a heteroplasmy of at least 2% are shown. (i) Depiction of unsupervised clustering of groups of cells based on shared somatic mtDNA mutations (y-axis) with corresponding individual mtDNA mutations (x-axis) associated with each cluster for the 500 cell input and (j) 800 cell input culture. Color bar, heteroplasmy (% allele frequency). (k) Fraction of cells (y-axis) carrying number of somatic mtDNA variants (x-axis) above indicated thresholds (≥1%, ≥5%, ≥10% heteroplasmy; red, black, and blue lines, respectively) for indicated cultures.