Quality control and cell type identification of scRNA-seq.

(A-C) UMAP of the 14,725 cells profiled here, with each cell color-coded for (A) Control or cKO, (B) the number of counts per barcode, and (C) the number of detected genes per cell. (D) Dot plot of marker genes. The dot plot shows the average expression level (the intensity of green) and percentage of expressed cells (the dot size). (E) UMAP of the 14,725 cells colored by cell type. (F) Monocle trajectories of neutrophils colored by pseudotime. (G) Monocle trajectories of neutrophils colored by cell type. Each dot represents a single cell. Cell orders are inferred from the expression of the most variable genes across all cells. Trajectory directions were determined by biological prior. (H) ROS generation of neutrophils in the spleen (Left) and peripheral blood (Right) of control (Ctrl) or <i>Map4k4</i>-cKO (cKO) mice; MFI, mean fluorescent intensity; ROS, reactive oxygen species; (n=6; mean ± SD). Mann-Whitney U test. (I) The percentage of phagocytic neutrophils in the spleen (Left) and peripheral blood (Right) of control (Ctrl) or <i>Map4k4</i>-cKO (cKO) mice; (n=6; mean ± SD). Mann-Whitney U test. (PDF)