SoxR and SoxS constitute an intracellular signal response system that rapidly detects changes in superoxide levels and modulates gene expression in E. coli. A time series microarray design was used to identify co-regulated SoxRS dependent and independent genes affected by superoxide Keywords: time course Overall design: To determine the immediate transcriptional response of E. coli to superoxide, we conducted a time series assay of mRNA levels immediately following the addition of paraquat. The wild type strain MG1655 and a strain with a precise deletion in soxR was grown in EZ Rich Defined Medium, a modification of Neidhardt’s defined rich medium. When cultures reached an OD600=0.5, 250µM paraquat (PQ) was added, a concentration that triggers the SoxRS transcriptional cascade, but only has a small effect on exponential growth rate in rich media. Samples were taken immediately before exposure to PQ, and every 2 minutes after exposure, for 10 minutes.