FIGURE 2.

Principal component analysis (PCA) of the transcriptome at different stages of growth. (A) Correlation between the first (PC1) and second (PC2) principal components of the transcriptome of samples taken in biological triplicate at different time points during E. coli growth in LB. The clustering of transcriptomes from the same time points confirms the reproducibility of our measurements. Furthermore, adjacent time points clustered close to each other forming a nearly complete cycle, the transcriptome measured at t = 0 being close to that measured at t = 7 h. (B) The temporal dependence of PC1 (circles) resembles that of E. coli growth (Figure 3A) suggesting that genes used for PC1 may play a role in adaptation to the exhaustion of nutrients, whereas the temporal dependence of PC2 (squares) resembles that of the culture pH (Supplementary Figure S4) suggesting that these genes may be involved in the adaptation to pH changes.