Extended Data Fig. 1: Quality control plots of CITE-seq data.

a) Bar plot showing the number of bone marrow (BM) cells collected from seven healthy pediatric donors aged 2.1-16.7 years (3 males, 4 females). From each sample, HSPC (CD235a⁻CD34⁺) and mesenchymal stromal cells (CD235a⁻CD45^loCD90⁺ or CD235a⁻CD45^loCD271⁺) were enriched by flow cytometry and combined with the non-enriched fraction from a genetically distinct donor. Pooled samples were subjected to CITE-seq using 138 oligonucleotide-conjugated antibodies, on the 10x Genomics platform. b) Boxplot of the percentage of mitochondrial reads per cell. c) Boxplot of the number of RNA counts per cell. d) Boxplot of the number of unique RNA features per cell. e) Boxplot of the number of ADT counts per cell. f) Boxplot of the number of unique ADT features per cell. g) Violin plot showing the relative expression level of the female-specific XIST gene per donor sample used to confirm sample sex. h) Violin plot showing the relative expression level of the male-specific UTY gene per donor sample used to confirm sample sex. i) CITE-seq-based weighted nearest neighbor uniform manifold approximation and projection (wwnUMAP) of cells from pediatric BM aspirates (n = 7) and adult BM aspirates (n = 2) per individual. Twenty-eight clusters were identified and annotated based on joint transcriptomic and protein expression patterns. MSC, mesenchymal stromal cell; HSC, hematopoietic stem cell; LMPP, lympho-myeloid primed progenitor; MEP, megakaryocyte-erythroid progenitor; MkP, megakaryocyte progenitor; EryP, erythroid progenitor; McP, mast cell progenitor; T_N, naive T cell, T_M: memory T cell; T_reg cell: regulatory T cell; MAIT cell: mucosal-associated invariant T cell; NK cell, natural killer cell; progDC, dendritic cell progenitor; cDC, conventional DC; pDC, plasmacytoid DC, Ery, erythroid; DC, dendritic cell.