Extended Data Fig. 8: Defining MGE-expressing populations of E. coli using M3-seq data.

a. UMAP of E. coli MG1655 transcriptomes from cells treated with the bacteriostatic antibiotics tetracycline and chloramphenicol. Colour gradient indicates normalized expression of pinQ, a marker gene for cluster 8 identified in Fig. 3e. b. Same as (A) but with colour gradient indicating normalized expression of tfaQ, a marker gene for cluster 13 identified in Fig. 3e. c. Same as (A) but with colour gradient indicating normalized expression of ydfK, a marker gene for cluster 12 identified in Fig. 3e. d. Same as (A) but with colour gradient indicating normalized expression of insI-2, a marker gene for cluster 16 identified in Fig. 3e. e. Plots of cells in principal component space for E. coli treated with bacteriostatic antibiotics, wherein the colour gradient indicates normalized pinQ expression. The principal component dimensions chosen for this analysis contained high loadings in genes that were upregulated in rare subpopulations (for example, pinQ, tfaQ). f. Same as (E) but with colour gradient indicating normalized tfaQ expression. g. Same as (E) but with colour gradient indicating normalized ydfK expression. h. Same as (E) but with colour gradient indicating normalized insI-2 expression. i. Kurtosis of all 100 computed principal components calculated from the single-cell transcriptomes of tetracycline- and chloramphenicol-treated E. coli MG1655. Notably, principal components with the highest kurtosis were not necessarily the same as those with the highest variance. j. Kurtosis of 15 principal components computed from tetracycline- and chloramphenicol-treated E. coli MG1655 cells, with individual curves corresponding to calculations from down-sampled subsets of cells with and without UMI counts scrambled among genes. Notably, scrambling abolishes the kurtosis signal and removes structure from clustering. Curves indicate mean values, and the shaded region the 95% confidence interval across N = 5 independent down-samplings. k. Same as (J) but for down-sampled subsets of cells with and without UMI counts scrambled among cells across N = 5 down-samplings.