Fig. 3

A time-course of Salmonella infection. a tSNE plot of induced single cells (perplexity = 10) computed based upon 32 Salmonella regulons. Color indicates Class I (purple) and Class II (orange). DBscan was used to cluster the cells into two groups. b The heatmap indicates Pearson’s correlation coefficients between the average Salmonella regulons expression of the partially induced, Class I, and Class II subpopulations. c tSNE plot (positioned as in Fig. 2e) colored by the pseudo-time order of the cells. The bar below indicates unexposed (gray), partially induced (green), Class I (purple), and Class II (orange) cells, ordered by pseudo-time. d Plot of normalized expression level of SPI-1 and SPI-2 regulons in single cells ordered according to pseudo-time and smoothed (see “Methods”). The bar below indicates partially induced (green), Class I (purple), and Class II (orange) cells, ordered by pseudo-time. e Bar chart indicating for each time-point (2.5, 4, and 8 h after infection), the fraction of the three identified subpopulations (partially induced, Class I, and Class II)