6 protocols
hybridization protocol
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)