Extended Data Fig. 6: Support information for cellular population dynamics in native hematopoiesis in vivo resolved by mtDNA based tracing.

(a) Assignment probabilities (%, colorbar) of scRNA-seq data derived transfer labels (rows) across mtscATAC-seq derived Louvian data clusters (columns) as identified in Fig. 6d. (b) Distribution of percent mitochondrial reads derived from mtscATAC-seq data (y axis) across PBMC populations (x axis). (c) Percent mitochondrial counts (y axis) in FACS sorted populations (x axis) from bulk RNA-seq data. (d) Identification of high confidence variants from CD34 + HSPC and PBMC cell populations. Number of variants passing both thresholds (dotted lines) is indicated. A Venn diagram depicts the overlap of shared mutations. (e) Percent duplicates of sequenced mtDNA fragments, mean mtDNA coverage and percent mitochondrial reads for CD34 + HSPC and PBMC cell populations as derived from mtscATAC-seq data. Boxplots: center line, median; box limits, first and third quartiles; whiskers, 1.5x interquartile range. (f) Distribution of maximum level of heteroplasmy of mgatk derived variants from (d) in individual cells. (g) 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/clone. (h) Fold-change (observed over expected) of identified rare mutations (y axis) in each class of mononucleotide and trinucleotide change from the CD34 + HSPC data. (i) Comparison of pseudobulk allele frequencies from mgatk identified variants (blue) and rare variants (green). Boxplots for (b,c,e): center line, median; box limits, first and third quartiles; whiskers, 1.5x interquartile range. Bounds are contained within the data range shown. Sample sizes exceed 100 single cells from one experiment.