scRNA-seq analysis of HSPC differentiation in mice surviving sepsis. (A) LSK cells classified as clusters of different cell states are shown by a UMAP plot of merged sham and CL&P datasets (left). Dot plots show expression of the cell-state specific marker genes in the classified clusters (right). (B) Left UMAP plots show classified clusters in sham and CL&P datasets, respectively. Right panel displays proportions of cells in each cell state. (C) Branchpoint analysis for LSK cells of merged sham and CL&P datasets inferred by Monocle 3. LSK cell manifold was colored by the pseudotime value (left) or by the cell state (right). Root (0) and leaf nodes (1–5) are shown with numbers; branchpoints are represented by green dots. (D) Expression of selected genes correlated with pseudotime. Cells are colored by sham or CL&P samples. (E) Distribution of sham LSK cells or CL&P LSK cells in different cell states over pseudotime. Root (0) and leaf nodes (1–5) are shown with numbers; branchpoints are represented by green dots. Frequencies of cells in the indicated pseudotime domains are shown.