Fig. 6

RNA velocity and trajectory analyses of lung monocyte and IM subpopulations in steady-state C57BL/6 mice. a t-SNE plot depicting the merged scRNA-seq data of lung CD64-expressing cells (see Fig. 1c), Ly-6C^lo patrolling monocytes (see Supplementary Fig. 9) and Ly-6C^hi classical monocytes (see Supplementary Fig. 12). b Prevalent patterns of RNA velocities substantiated by arrows and visualized on the same t-SNE plot as shown in (a). Right panel shows a higher magnification of the area depicted by a black dashed line in the left panel. (see single cell velocities in Supplementary Fig. 13). c Violin plot showing quantification of single cell relative 2D velocities in the indicated cell (sub)populations, as presented in Supplementary Fig. 13. d Visualization of single-step transition probabilities from Ly-6C^lo patrolling monocytes (left), Ly-6C^hi classical monocytes (middle) or CD64⁺CD16.2⁺ monocytes (right) to neighboring cells. Ellipses represent 95% confidence. e, f Slingshot analysis of Ly-6C^lo patrolling monocytes, CD64⁺CD16.2⁺ monocytes, and neighboring CD206⁻ IM. e Suggested pseudo-time trajectory from Ly-6C^lo patrolling monocytes to CD206⁻ IM. Ellipses represent 80% confidence. f Heatmap depicting gene expression profiles of Ly-6C^lo patrolling monocytes, CD64⁺CD16.2⁺ monocytes, and neighboring CD206⁻ IM ordered according to Slingshot pseudo-time trajectory. Left color bars indicate annotation by cell type