Fig. 2

Human Lin− compartment investigation by means of CD34/CD164 fractionating. a Gating strategy for the FACS sorting of four subsets inside the Lin—fraction of a healthy donor BM, according to CD34 and CD164 expression (left panels). Relative contribution of CD71+ progenitors is shown in the right panels. b SPRING plot of the four Lin−CD34/CD164 subsets single-cell transcriptomes. Each point is one cell. Labels at the edges represent the transcriptional states associated to early lineage commitment (P, early progenitor cells; Meg, megakaryocytes; E, erythroid cells; BaP, basophil progenitors; N, neutrophils; M, monocytes; DC, dendritic cells; Ly-T/B/NK, lymphoid T/B/NK cells). Color legend as in a. Gene expression maps are available in Supplementary Fig. 4. c Predicted hierarchy based on two steps PBA. d Classification of individual cells into homogenous transcriptional groups numbered from 1 to 15, based on inferred principal trajectories. Solid lines show results based on final converged iteration (Supplementary Fig. 3b for details). Dashed lines added manually to highlight a potential additional trajectory not present in final iteration and inferred by visual inspection (DC-M). e Gene dynamics associated to branching and fate decisions. Plots on the left, branching and groups; mirror heatmaps, expression of statistically significant genes differentially expressed along each branch pseudotime (LRT adjusted p value < 0.05). Plots on the right, a selection of three transcription factors differentially expressed along each branch (LRT adjusted p value < 0.05). f Projection of the transcriptional states of the seven HSPCs onto the Lin−CD34/CD164 map