Extended Data Fig. 10: scRNA-seq characterization of stimulated bone-marrow mononuclear cells.

BM mononuclear cells incubated in HSC cytokine-rich media with no treatment (NT) or 100 ng/mL LPS or Pam3CSK4 (Pam3) for 4 days. Cells (n = 8,702) are visualized on a UMAP projection and colored by (a) treatment, (b) Leiden clusters, and (c) cell-type annotations. (d) Matrixplot showing the mean log-transformed UMI counts of the top 5 differentially expressed genes (FDR < 0.01, two-tailed Wilcoxon rank-sum test) for each cluster in (b). (e) Heatmap showing differentially expressed genes (FDR < 0.01, two-tailed Wilcoxon rank-sum test) between clusters 3 (CD14 monocytes, n = 786 cells) and 14 (iMS1 cluster, n = 130 cells). (f) UMAP projections of non-stimulated BM myeloid and progenitor cells (HSC/MPP, CMP, GMP, Mono; n = 1,976 cells total) colored by cell type (left) and diffusion pseudotime (right). (g) Violin plots showing pseudotime values for each cell type in each stimulation condition. n = 1,976 and 901 cells for NT and LPS or Pam3 treatments, respectively. Violin plots show a kernel density estimate of the data, using Scott’s rule to calculate the appropriate kernel bandwidth. The violin extends to 2x the bandwidth in both directions. (h) Volcano plots showing differentially expressed genes between LPS or Pam3CSK4 and untreated cells for the HSC/MPP (n = 1,168 cells) and GMP populations (n = 519 cells). Differentially expressed genes (logFC > 0.3, p < 0.05; two-sided Wilcoxon rank-sum test) are shown in red. Known receptors (based on a previously published database⁵¹) that are differentially expressed are labelled. HSC/MPP, hematopoietic stem cells and multipotent progenitors; CMP, common myeloid progenitors; GMP, granulocyte-macrophage progenitor; MEP, megakaryocyte-erythroid progenitors; MYL, myeloblasts; RBC, red blood cells.