"55 min after turning off oxygen"	"characteristics_ch1.1"
"completely aerobic conditions"	"characteristics_ch2.1"
"Two color cDNA microarray data are never devoid of spurious technical contributions that"	"data_processing.1"
"originate during array printing, as well as during the collection and processing of samples,"	"data_processing.2"
"fluorescent labeling and hybridization and scanning of the microarray images (Balazsi et al."	"data_processing.3"
"2003, PNAS). To minimize the effect of such contributions, microarray data were"	"data_processing.4"
"normalized as described before (Tong et al. 2004 BBRC). Briefly, spots were excluded from"	"data_processing.5"
"further analysis if the foreground intensity of less than 50% of the pixels within the spot"	"data_processing.6"
"were above 2 standard deviations of the background. We generated expression data tables"	"data_processing.7"
"in Microsoft Excel, containing the following information for each of the 14,352 entries: block"	"data_processing.8"
"(B), column (X), and row (Y) number, red foreground (f_r) and background (b_r), green"	"data_processing.9"
"foreground (f_g) and background (b_g) intensity. The position of each probe within a block,"	"data_processing.10"
"P is defined by the pair of integers (X,Y). Log ratios were defined as the base 10 logarithm"	"data_processing.11"
"of (F_r-B_r)/(F_g-B_g), where F_r, B_r, F_g and B_g represent the median Cy5 (red)"	"data_processing.12"
"foreground and background, and the median Cy3 (green) foreground and background"	"data_processing.13"
"intensities, respectively. In some cases, when the intensity of the background was higher"	"data_processing.14"
"than or equal to the intensity of the foreground, the resulting log ratios became complex or"	"data_processing.15"
"infinity. These values were eliminated using the find, imag, and isfinite functions in Matlab."	"data_processing.16"
"Next, data were normalized, by averaging the log ratios resulting from all spots printed by a"	"data_processing.17"
"print tip, and subtracting the resulting average from all the individual log ratios"	"data_processing.18"
"corresponding to the same tip. Finally, all the log ratios of the same gene from each slide"	"data_processing.19"
"were averaged and listed in a new file."	"data_processing.20"
"Epicentre MasterPure RNA isolation Kit, Madison, WI"	"extract_protocol_ch1.1"
"Epicentre MasterPure RNA isolation Kit, Madison, WI"	"extract_protocol_ch2.1"
"Escherichia coli"	"organism_ch1.1"
"Escherichia coli"	"organism_ch2.1"
"E coli, 55 min"	"source_name_ch1.1"
"E coli, 0 min"	"source_name_ch2.1"
"ecoli_aerobicanaerobic_55min_rep1"	"title.1"
"55 min after turning off oxygen"	"characteristics_ch1.1"
"completely aerobic conditions"	"characteristics_ch2.1"
"Escherichia coli"	"organism_ch1.1"
"Escherichia coli"	"organism_ch2.1"
"E coli, 55 min"	"source_name_ch1.1"
"E coli, 0 min"	"source_name_ch2.1"