Supplementary Figure 4: Assembly of the hematopoietic core dataset.

a, In silico lineage depletion of hematopoietic progenitors derived from tiers 3, 5, 6 and 7 to generate the hematopoietic core dataset. Each lineage dictates a score based on expression of its enriched genes. Red lines represent score cutoffs determined for depletion (Methods). b, MetaCell analysis of the core dataset. Meta-cell annotation as in Fig. 3b. c, Co-clustering of the core dataset. Values indicate how likely two cells are to belong to the same meta-cell in bootstrap analysis. d, Distribution of tier 7 cells on the core meta-cells. Columns represent meta-cells of the core dataset. Top bars indicate the fraction of each core meta-cell in tier 7. Heat-map shows fold change of mean expression of HSC related genes across tier 7 meta-cells. Apoe and Gata2 mark erythroid/megakaryocyte priming. * marks the stringent HSC definition. e, Differential gene expression (log₂ of pooled size-normalized expression) between cells from stringent HSC and the rest of the hematopoietic core dataset. Dashed lines indicate a 2-fold threshold. f, Correlation between stem-score (x axis) and proliferation signature (y axis) in single cells. Dashed lines represent stratification by top stem-score percentiles. g, Dormancy quantification by a label retaining assay, where GFP expression of H2B-GFP mice was inhibited by doxycycline administration for 150 days. h, Expression of genes defining the stem-score in label retaining cells (LRC), non-LR HSC and MPP1. n = 3 independent experiments, horizontal lines indicate mean (Supplementary Table 5). i, Expression patterns of prominent marker genes and transcription factors on the core model. j, Pairwise Pearson correlations across core meta-cells of erythrocyte and lymphoid/myeloid transcription factors with themselves (left) and non-transcription factors genes (right). n = 50 meta-cells over 9,307 single cells.