Extended Data Fig. 1: Sample preparation, quality controls, and related parameters and results related to scRNA-seq analysis.

a, Fluorescence-activated cell sorting (FACS) strategy for scRNA-seq sample preparation. b, Summary of sample information. c, Cell viability percentages immediately before cells were loaded into the 10X Chromium Controller. d, Representative GEM formation after the 10X Chromium Controller under the microscope. e, Violin plots of the number of genes, number of UMIs, mitochondria count percentage, and UMI per gene of all QC-passed cells in different organs. f, Uniform manifold approximation and projection (UMAP) of 19,582 cells from the bone marrow (BM), peripheral blood (PB), and spleen (SP) colored by sample origin and cell type, respectively. Expression of unique genes specifically distinguished each cluster and associated them with neutrophils (Neu) (S100a8 and S100a9), myeloid progenitors (MP) (Cd34, Kit, Mpo and Elane), hematopoietic stem progenitor cells (HSPC, not including MP) (Cd34, Kit, Mpo^- and Elane^-), monocytes (Mono) (S100a4 and Ccl9/MIP-1γ), B cells (Cd79a and Cd79b), T cells (Cd3d and Ccl5), and dendritic cells (DC) (Siglech), respectively. Cont: contaminated cells. g, Heatmap showing the five highest differentially expressed genes (DEGs) per cell type for all QC-passed cells. h, As in e but using only neutrophils in different organs. i, Comparison of Gr1⁺ BM neutrophil populations in our data with Ly6g⁺ BM neutrophil populations in Dr. Ido Amit’s data. Cluster labels are transferred from our data to Dr. Ido Amit’s data¹³(Methods). Left: UMAPs of 3591 Gr1⁺ neutrophils and 2304 Ly6g⁺ neutrophils colored by data set or cluster identity. Right: Neutrophil compositions in our data and Dr. Ido Amit’s data. j, Violin plots of the number of genes and number of UMIs of our Gr1⁺ neutrophils and Dr. Ido Amit’s Ly6g⁺ neutrophils.