Fig. 1: Generating single-cell transcriptomes from neutrophils across multiple biological tissues.
a Overview of the experiment. Neutrophils were isolated from 6–8-week-old B6 mice from blood, bone marrow and spleen, stained for Ly6G and CD11b, and sorted, followed by droplet-based scRNA-seq using the 10X platform. Two independent experiments of healthy tissues were performed with N = 3 mice pooled for each tissue per experiment, totaling N = 12,619 cells, which were combined for analysis. b UMAP plot including all healthy neutrophils, partitioned exemplarily into four populations P1–P4. For smaller or larger numbers of populations, see Supplementary Fig. 3. c Marker gene expression in the 4-population model. Marker genes were identified by Wilcoxon Rank Sum test (two-tailed) using the Seurat function “FindAllMarkers” with standard settings; only genes with loge fold change ≥ 0.25 and Bonferroni adjusted p-value ≤ 0.05 are shown. d UMAP embedding of all cells colored by tissue of origin. e Abundance of populations across organs. Neutrophils colorized by: G2M cell cycle score (f), percentage of features in top 500 features (g) and preNeu score (h). i Frequency of preNeu across tissues. j G2M cell cycle score in preNeu and remaining cells in each tissue. Unpaired t-test (two-tailed) between preNeu and all other neutrophils within each tissue. k G2M cell cycle score of preNeu across tissues. ANOVA followed by unpaired t-test was used to compare the G2M cell cycle score between preNeu and other neutrophils in each tissue.
