Identification of transcriptomes associated with altered biological processes in LSK cells after infection. Related to Fig. 3. (A) Volcano plot shows differentially expressed transcripts (1.8-fold change threshold, FDR < 0.05) upregulated in sham cells (red) or in CL&P cells (blue). (B) Biological process– and pathway–associated genes upregulated in CL&P cells. (C) Biological processes and pathway-associated genes downregulated in CL&P cells. (D) UMAP projection of the cell cycle phases of sham and CL&P LSK cells shown by expression of Pcna and Ccnb2. (E) Proportions of sham and CL&P LSK cells in each cell cycle phase. (F) Representative plots display the gating of HSPC subsets and measurement of proliferation via Ki67 expression and DNA content. (G) Percentages of HSCs and MPP cells in the G0 phase of the cell cycle are shown, with symbols depicting data of individual mice (sham = 5, CL&P = 3) and bars showing the mean value ± SD. *P < 0.05; ** P < 0.01; ns, P > 0.05 (unpaired two-tailed Student’s t test). (H) Violin plots of transcript expression values for the indicated genes in sham and CL&P LSK cells in the indicated cell cycle phases. (I) Specification of the trajectory leaf nodes on the pseudotime domains of merged sham and CL&P datasets. (J) Trajectory UMAP projection of scaled expression of core signatures of each leaf node of merged sham and CL&P datasets. (K) Scatterplots display co-expression of the lymphoid-specific gene Dntt and the myeloid-specific gene Ctsg.