Affymetrix Generic Hybridization
The quality of the raw images (.DAT files) and their averaged intensity (.CEL files) were analyzed using the affy package of Bioconductor (25) implemented in the R statistical language. The expression values of all samples were calculated from raw intensity .CEL files using the expresso function, which performed background correction using robust multi-array average (RMA) method, normalization using the quantiles method, probe specific PM / MM correction using the pmonly method, and summary expression values using the medianpolish method.
E. coli MG1655 was grown in MOPS minimal glucose medium at 37 degrees C with aeration to an OD600 of 0.4 - 0.5, and HOCl was added to a final concentration of 400 uM. 0.5 ml samples were collected in liquid nitrogen immediately before, 5 min after, and 10 min after HOCl addition
(Parameters: start time = 0, stop time = 7, time unit = hours, min temperature = 37, temperature unit = C, media = MOPS glucose medium)
total RNA was prepared using the Rneasy Midi kit (Qiagen)
(Parameters: Extracted product = total_RNA, Amplification = none)
performed according to Affymetrix guidelines at the Affymetrix and Microarray Core facility at the University of Michigan, Ann Arbor
(Parameters: Amplification = none, Mass unit = Micro gram)