"genotype: rpoN mutant (EcJR-8)"	"characteristics_ch1.1"
"growth protocol: logarithmic phase in DMEM-MOPS"	"characteristics_ch1.2"
"genotype: wild type"	"characteristics_ch2.1"
"growth protocol: logarithmic phase in DMEM-MOPS"	"characteristics_ch2.2"
"The microarray data were analyzed using R (v. 2.2.1) and the MAANOVA (v. 0.98.8) package. Raw intensity values from replicate probes were averaged and log2 transformed after normalization with the pin-tip LOWESS method. The normalized intensity values were fitted to a mixed model ANOVA considering array and biological replicates as random factors and dye, strain and growth phase as fixed factors. The linear model tested was Y (intensity) = array + dye + strain (wild type or mutant) + growth phase (exponential or stationary) + strain*growth phase + sample (biological replicate) + error. Significant differences in expression due to strain, growth phase and strain*growth phase were determined using the Fs test in MAANOVA which uses a shrinkage estimator for gene-specific variance components that makes no assumption about the variances across genes with 500 random permutations to estimate the p-values. The q-value package in R was used for determining the false discovery rate (FDR)."	"data_processing.1"
"5mL of culture was mixed with 5mL of hot acid phenol:chloroform. Samples were held at 65ºC with periodic shaking for at least 10 minutes before centrifuging at 4000 rpm for 20 min. Supernatant was extracted again with acid-phenol:chloroform and then with chloroform:isoamyl alcohol (24.1). RNA was precipitated overnight at –80ºC in 2.5V 100% ethanol and 1/10V 3M sodium acetate pH 5.2. RNA samples were purified and treated with DNase using the Rneasy kit (Qiagen)."	"extract_protocol_ch1.1"
"5mL of culture was mixed with 5mL of hot acid phenol:chloroform. Samples were held at 65ºC with periodic shaking for at least 10 minutes before centrifuging at 4000 rpm for 20 min. Supernatant was extracted again with acid-phenol:chloroform and then with chloroform:isoamyl alcohol (24.1). RNA was precipitated overnight at –80ºC in 2.5V 100% ethanol and 1/10V 3M sodium acetate pH 5.2. RNA samples were purified and treated with DNase using the Rneasy kit (Qiagen)."	"extract_protocol_ch2.1"
"EcJR-8 grown to OD600 = 0.5 in DMEM-MOPS 0.4% glucose at a 10:1 flask-to-media volume in a rotary shaker (180 RPM)."	"growth_protocol_ch1.1"
"Escherichia coli O157:H7 str. Sakai"	"organism_ch1.1"
"Escherichia coli O157:H7 str. Sakai"	"organism_ch2.1"
"rpoN mutant grown to logarithmic phase"	"source_name_ch1.1"
"wild type grown to logarithmic phase"	"source_name_ch2.1"
"Logarithmic phase sample 3"	"title.1"
"genotype: rpoN mutant (EcJR-8)"	"characteristics_ch1.1"
"growth protocol: logarithmic phase in DMEM-MOPS"	"characteristics_ch1.2"
"genotype: wild type"	"characteristics_ch2.1"
"growth protocol: logarithmic phase in DMEM-MOPS"	"characteristics_ch2.2"
"EcJR-8 grown to OD600 = 0.5 in DMEM-MOPS 0.4% glucose at a 10:1 flask-to-media volume in a rotary shaker (180 RPM)."	"growth_protocol_ch1.1"
"Escherichia coli O157:H7 str. Sakai"	"organism_ch1.1"
"Escherichia coli O157:H7 str. Sakai"	"organism_ch2.1"
"rpoN mutant grown to logarithmic phase"	"source_name_ch1.1"
"wild type grown to logarithmic phase"	"source_name_ch2.1"