Extended Data Fig. 5: M3-seq profiling during exponential growth and early stationary phase.

a. UMAPs of E. coli MG1655 transcriptomes in exponential and early stationary phase (top) and associated clustering (bottom, set to the lowest clustering resolution parameter). Clustering set at the lowest resolution parameter. Axes denote the first two UMAP components. b. Same as (A) but for E. coli Nissle. c. Same as (A) but for B. subtilis 168. d. GO term enrichment of select biological process calculated with marker genes identified for populations of exponential and stationary phase E. coli MG1655 identified in (A). Marker genes were determined as described in Materials and Methods. The p-values are -log₁₀ transformed such that the most strongly enriched biological processes have the highest score. Selected processes were those with the lowest p-values after thresholding at 0.05. Enrichments for exponential and stationary phase cells include expected processes (green and red, respectively), including growth related and energy generation processes (exponential) and those involving secondary carbon metabolism and the TCA cycle (stationary). e. Same as (D) but for E. coli Nissle. Similar to E. coli MG1655, enrichments include expected processes (green for exponential; red for stationary). f. Same as (D) but for B. subtilis 168. Similar to E. coli, enrichments include expected processes (green for exponential; red for stationary).