Gene expression timecourse in ΔrpaA strain

The goal of the experiment was to determine whether gene expression oscillates in the absence of rpaA. It was reported previously (e.g., Takai et al, PNAS 2006) that activity of a handful of individual expression reporters was arrythmic, and we conducted this microarray timecourse to determine whether expression is arrhythmic geneome-wide. Cultures were grown in a turbidostat as described previously (Vijayan et al, PNAS 2009). Cultures were entrained with two consecutive light/dark cycles and released into continuous light at time T = 0. Cultures were samples every 4 hours for 48 h between T = 24 h and T = 72 h, inclusive. Gene expression at each timepoint was compared to the time-averaged gene expression (determined using a pool of equal mass quantities of RNA from all timepoints) using a two-color Agilent microarray.