Figure 3

Gene expression profile of FACS isolated E. coli persisters. E. coli ASV Cells were sorted as described in legend, Fig. 2. cDNA was prepared from the total RNA and hybridized to spotted E. coli DNA microarrays [16]. Data shown are the averages of three independent biological replicates. Genes up-regulated in persisters are indicated as red and those genes which are repressed as green. The differential expressed genes are identified according to the procedures described in Materials and Methods. (A) Gene expression and spot intensities of sorted persisters (P) compared to sorted non-persisters (Q) from an exponential growth phase cell culture. (B) Gene expression and spot intensities of sorted persisters (P) compared to stationary phase (S) cells. (C) Heat map comparison of representative genes differentially expressed in persisters (P) or stationary (S) phase cells as compared to non-persisters (Q) and exponential growth phase cells (L), respectively. Genes are considered differentially expressed if the local intensity-dependent Z-score is greater than 1.96 or less than -1.96 and the expression log2 (ratio) is more than 1 or less than -1. The gene names are shown on the right, together with the functional groups.