Extended Data Fig. 3: scWB convalescent sepsis neutrophil analysis and scHSPC hematopoietic stem and progenitor cell (HSPC) RNA based identity mapping.

a, Boxplots of proportions of neutrophil states in HC vs. convalescent sepsis samples from scWB. Boxplots denote minimum and maximum with whiskers and bottom quartile, median and upper quartile with the box. b, Proliferative fraction of anti-CD3/28 bead-stimulated CD4⁺ T cells after co-culture with neutrophils at a 4 neutrophil:1 T cell ratio, compared to positive controls of CD4+ T cells cultured with anti-CD3/28 beads alone (n = 10 HC, n = 9 convalescent sepsis). Boxplots denote minimum and maximum with whiskers and bottom quartile, median and upper quartile with the box. c,d, HSPC (right) mapping to (c) Seurat bone marrow mononuclear cell (BMMC) dataset²⁴ (left) and (d) healthy donor BMMC dataset from Granja et al.²⁵ (left). e, UMAP of HSPCs clustered on Harmony batch corrected RNA and chromatin reduced dimensions after non-HSPCs were filtered out (46,156 cells; Methods). f, UMAP colored by RNA prediction identities from HSPC mapping to Seurat BMMC dataset. g, UMAP of progenitor cells alone clustered on Harmony batch corrected RNA and chromatin reduced dimensions (16,820 cells; Methods). h, Boxplots of progenitor cell clusters as a proportion of total progenitor cells (n = 15 acute sepsis, n = 7 HC). Boxplots denote minimum and maximum with whiskers and bottom quartile, median and upper quartile with the box. i, Heat map of genes defining progenitor clusters with known lineage defining genes highlighted. j, Boxplots of HSC clusters as a proportion of total HSCs (n = 15 acute sepsis, n = 7 HC). Boxplots denote minimum and maximum with whiskers and bottom quartile, median and upper quartile with the box. k, UMAP of CD34⁺ HSPCs from annotated Human Cell Atlas bone marrow mononuclear cell (BMMC) scRNA-seq data²⁶ for deriving granulopoiesis gene set (Methods). Neu, neutrophils; c/pDC, conventional/plasmacytoid dendritic cell; GMP, granulocyte monocyte progenitor; LMPP, lymphoid-primed multipotential progenitors; NK, natural killer; Prog, progenitor; Mk, megakaryocyte; RBC, red blood cell; Eryth, erythrocyte; CMP, common myeloid progenitor; Mono, monocyte; CD4 N1/2, CD4+ naïve T cell 1/2; CD4 M, memory CD4+ T cell; CD8 CM, central memory CD8+ T cell; PC, plasma cell; MDP, monocyte/dendritic cell progenitor; MultiLin, multilineage progenitor; MEP, megakaryocyte/erythroid progenitor; MKP megakaryocyte progenitor; ERP, erythrocyte progenitor; Eo, eosinophil; Mast, mast cell.