Extended Data Fig. 5: Supporting analyses for PT3 bone marrow mononuclear cell ASAP-seq dataset.

(a) Projection of select protein-derived antibody tag abundances for indicated proteins. Select arrows indicate populations positive for the respective marker. UMAP coordinates same as Fig. 6c. (b) Projection of protein surface markers CD56 (NK cells and MDS-associated cells) and CD335 (only NK cells) with arrows indicating the two cell populations. (c) UMAP of ASAP-seq processed bone marrow mononuclear cells from a PS (top) and a healthy control¹¹ (bottom) with hematopoietic stem and progenitor cells (‘progenitors’) indicated in the red boxes. (d) Projection of protein tags within the boxed progenitor populations as in (c), contrasting the presence of only CD71⁺ cells among CD34⁺/c-Kit⁺ cells in PS as compared to the healthy control. (e) Volcano plot showing differential gene activity scores for CD8 recent thymic emigrants (RTEs) compared to other CD8 naive T cells. Annotated genes in red represent known marker genes for RTEs. (f) Zoom (top) and mtDNA deletion heteroplasmy (bottom) in differentiated CD8 T and NK cells from the BMMNC populations. (g) Volcano plot illustrating the association between protein levels and mtDNA deletion heteroplasmy in single cells. P-values were computed from the default two-sided Seurat Wilcoxon test with Bonferroni p-value adjustment. (h) Projection of cell state surface markers (CD3, CD8) and top antibody tags (CD16, CD195) as determined in (g). (i,j) Reclustering and UMAP depiction of PT3 PBMC mtscATAC-seq data identify (i) low heteroplasmy and (j) recent thymic emigrants (RTEs). Cell type annotations as indicated. (k) Landscape of 69 heteroplasmic somatic mtDNA mutations identified in BMMNC. Statistical test: two-sided Fisher’s exact test. (l) Substitution rate of mgatk identified heteroplasmic mutations (y-axis) in each class of mononucleotide and trinucleotide change resolved by the heavy (H) and light (L) strands of the mitochondrial genome. (m) Scatter plot of 69 somatic mtDNA variants identified in panel (l) stratified based on cells annotated as del7q (x-axis) and wild type for chr7 (y-axis). (n) Projection of wild type (diploid chr7)-enriched somatic mtDNA mutations m.14476G > A (50%) and m.12242A > G (25%).