Extended Data Fig. 9: Growth and gene expression in E. coli cells infected with λ phage.

a. Growth and gene expression in E. coli cells infected with λ phage. A. Plot depicts growth of E. coli grown to early exponential phase (OD ~ 0.2–0.3) and infected with λ phage (MOI ~ 100) or supplemented with phage vehicle (LB). Curves indicate mean values, and shaded error bars are 95% confidence intervals. b. Replicate plaque assays of λ phage grown on E. coli MG1655 without magnesium (the same conditions used in phage infection experiments eBW4). c. Pseudobulk comparison of the infected sample compared to an exponential phase control. Each point represents a single gene, and the red dots represent λ phage genes. d. Zero-centered and normalized expression of all observed λ genes for each cluster identified in Fig. 5b. Genes displayed were those genes which had more than 10 UMIs across the entire population. Expression of λ genes is strongly enriched in the lytic cluster (3) but lower in the rest of the population. e. Boxplot of E. coli and λ UMIs/cell of lytic (1189 cells) and non-lytic cells (8195 cells). Boxplot limits are as defined in Materials and Methods. We report a median of 57 ± 35 E. coli UMIs, 0 ± 0 λ UMIS for non-lytic cells, and 55 ± 34 E. coli UMIs, 18 ± 14 λ UMIs for lytic cells. Data was collected in a single sequencing experiment (N = 1). f. Volcano plot of all host genes when comparing the cells in the lytic cluster to cells outside the cluster. Fold changes and p-values were computed using the FindMarkers function in Seurat, where the ‘min.pct’ and ‘logfc.threshold’ were both set to 0. g. UMAP of phage infected cells generated using alignments to only the E. coli MG1655 genome. Colors indicate sampling timepoint after infection. h. Same as (G) but with colors indicating clusters of transcriptionally similar cells assigned after re-performing clustering with only E. coli transcripts. i. Same as (G) but with colour gradient indicating normalized λ phage UMI count in each cell. j. Boxplots of normalized λ UMI count across each cluster in (H) (N = 4215, 2885, 2075, 209 cells). Boxplot limits are as defined in Materials and Methods. k. Silhouette scores computed using the principal components of the lytic cluster (see Fig. 5b, c) and of ‘null subpopulation’ which is a random sample of cells across each alignment.