Extended Data Fig. 1: scWB single-cell RNA and cell surface profiling annotation, clustering and neutrophil RNA velocity analysis.

a, UMAP of 272,993 cells with TotalVI denoised surface protein marker expression overlaid for selected lineage defining markers. b, Cell surface expression of proteins denoting neutrophil maturation stages for annotated neutrophil subsets. Boxplots denote minimum and maximum with whiskers and bottom quartile, median and upper quartile with the box. c, Comparison of broad annotations (Methods ‘Whole blood single cell multi-omic analysis (scWB)’) with data driven algorithmic labeling of cell identity by SingleR based on reference bulk RNA-seq profiles of pure cell populations from the Blueprint Consortium. d, Proportions of neutrophils and lymphocytes and HLA-DRA and HLA-DRB1 gene expression in classical monocytes in healthy controls (HC) (n = 6), sepsis (n = 26) and post-cardiac surgery (CS) (n = 7) samples. Boxplots denote minimum and maximum with whiskers and bottom quartile, median and upper quartile with the box. e, Clustering results at varying resolutions (0.8–1.1) for fine annotation strategy. f–i, Heat maps of gene markers for (f) PADI4+ immature neutrophils (g) IL1R2+ immature neutrophils (h) MPO+ immature neutrophils/progenitors and (i) cycling neutrophil progenitors. j, UMAP of neutrophils (excluding degranulating neutrophils) with RNA velocity stream directions plotted. k, Partition-based graph abstraction analysis of RNA velocity predicted cellular trajectory transitions. Neu, neutrophils.