Fig. 5: The lineage realization and kinetics of each meta-clone is determined by its early transcriptomic signatures.

a Stacked distribution of cell counts in percentage view where the x axis shows the proportion of cell counts for each population, the y axis shows the meta-clones, and the number at the side of each bar is the total counts for each meta-clone. b Distribution of late progenitors at day 6 for meta-clones 0 and 1. c Left: only cells from the earliest progenitor populations were used for DEGs analysis, which is prog_1, as shown with brown color in the UMAP landscape for all cells. Right, examples of meta-clone-specific UMAPs. d Volcano plot of DEGs between prog_1 cells within meta-clone 1 and meta-clone 0. Identified genes associated with specific terminal states (Chek1, Cited2, Pcna), Thy1, Cd48). e Examples of gene expression violin plots for prog_1 cells for Chek1, Pcna, F2r and Nfix, illustrating early lineage expression in the most primitive progenitor population. f Left: only cells from the progenitor 2 populations were used for DEGs analysis, as shown with pink color in the UMAP landscape for all cells. Right, examples of meta-clone-specific UMAPs. g Volcano plot of DEGs between prog_2 cells within meta-clone 1 and meta-clone 0. Lineage specific gene expression can be seen, Gfi1, Alox5, Cebpe, Cd200r and S1pr4. h Examples of gene expression violin plots for prog_2 cells (Irf8, Csf1r, Gfi1 and Cebpe). i Volcano plots of DEGs between prog_1 cells within meta-clone 5 vs rest and meta-clone 8 vs rest. Upregulated genes are mostly associated with the stemness of a cell (e.g., B2m, Hmga2). d,g,i Wilcoxon rank-sum two-sided test was used to calculate the DEGs between same identity of cells from different meta-clones.