a) UMAP highlighting the selected HSC clusters (HSC 1–3, left panel). Differential gene expression between WT (n = 2,150 cells) and Tet2 KO (n = 2,989 cells, central panel) or WT and Dnmt3a KO (n = 1,325 cells, right panel) HSC 1–3 clusters. Red dots represent differentially expressed genes (permutation test followed by Benjamini-Hochberg (BH) correction, FDR < 0.05, see online methods) with an absolute log2 fold change higher than 0.5. Pathway enrichment was performed with EnrichR57. b) Top panel: heatmap showing single cells from HSC 1–3 clusters. Bottom panel: Generalized additive model fit for erythroid, myelo-monocytic and stem scores from WT (n = 7 mice) HSC 1–3 clusters (n = 7,648 cells). Grey areas represent the 95% confidence interval. c) For each genotype, 1,225 cells from the HSC 1–3 clusters were randomly sampled and density plots were generated. The percentage of cells with either erythroid or myelo-monocytic priming is shown. d) Transcriptional priming scores for HSC 1–3 cells for Tet2 KO (2,989 cells; n = 7 mice), WT (2,150 cells; n = 7 mice) and Dnmt3a KO (1,225 cells, n = 4 mice) progenitors (two-sided Wilcoxon rank sum test followed by Bonferroni correction). e) Posterior probabilities of Gaussian mixture model fit for myelo-monocytic transcriptional priming for 1,225 randomly sampled cells from the HSC 1–3 clusters for WT (n = 4), Tet2 KO (n = 3) or Dnmt3a KO (n = 4) from Chromium samples (Binomial test). f) In vitro colony-forming assay using purified LT-HSCs from WT (n = 282 colonies), Tet2 KO (n = 391 colonies) or Dnmt3a KO (n = 209 colonies; two-sided Fisher exact test; CFU-GM = colony-forming unit granulocytic/monocytic; BFU-E = burst-forming unit erythroid; CFU-GEMM = colony-forming unit granulocytic/erythroid/monocyte/megakaryocyte, see online methods). g) Schematic representation of the procedure for visualization of the differentiation topology. h) Differentiation topologies derived from scRNA-seq data.