Fig. 8.

Genome-wide RNAP occupancy changes in MG1655 upon progressive MG accumulation in Type III experiments. ChIP-chip signals for test DNA (cAMP-treated) at t_30min (A), t_60min (B), t_120min (C) and t_240min (D) was compared in silico to test signals at t_10min, thus visually eliminating cAMP-induced changes and highlighting MG induced changes in RNAP occupancy. For each time point Cy5 signal intensities were averaged from two independent replicates and log₂ ratios were calculated. Log₂ ratios were then normalized with respect to eight reference regions across the genome that exhibited low signal intensities in both cAMP-treated and untreated cells and that did not change over time (see Supporting information). For a complete list of significant changes see Table S3.