Fig 1: A continuum of differentiation outputs and transcriptomes within the human HSC/MPP pool and 49f+ HSCs compartments. a, d Percentage of colonies of the indicated type derived from HSC/MPP pool single cells (n = 435 colonies from six independent CBs) (a) and from 49f+ HSCs (n = 819 colonies from four independent CBs) (d); mean ± SEM is shown. b, c, e, f, Principal component analysis (PCA) of the surface marker expression at the time of sort of single HSC/MPP pool cells (n = 435 colonies from six independent CBs) (b, c) and of 49f+ HSCs (n = 714 colonies from four independent CBs) (e, f). Colours indicate the type of differentiated colony produced by each single-cell after culture. Density plots (top panel) and boxplots (bottom panel) of PC1 (b, e), and PC2 values (right panel, e) from single cells producing indicated types of differentiated colonies; *p < 0.05 by Kruskal–Wallis test with multiple comparisons. c, f Cell surface markers with the highest PC loadings are shown. g Mean time to first division of single cells producing colonies containing the indicated cell types (EC50 of non-linear fit of cumulative first division kinetics); n = 4 independent experiments each with an independent CB (with respectively 19, 98, 34, 230 single cells per experiment), ***p < 0.001 by two-sided paired t-test. h Normalised cell surface expression of CLEC9A (left) and CD34 (right) at the time of sort (same HSC/MPP pool cells as in b) for single cells producing the indicated types of differentiated colonies. Of note, in e and h, My/NK/Ery includes My/NK/Ery and My/NK/Ery/Meg colonies. **p < 0.01 by Kruskal–Wallis test with multiple comparisons. i–k Single-cell RNA-seq analysis of 49f+ HSCs (n = 169 single cells that passed quality control). i, j Cell surface expression of CLEC9A (i) and CD34 (j) overlaid on the tSNE representation of 49f+ HSCs. k Cell surface expression levels of CLEC9A (left) and CD34 (right) in the 49f+ HSCs of the indicated ICGS clusters; ***p < 0.001 by two-sided unpaired t-test. All boxplots show median, interquartile and 5–95 percentile