"strain: e. coli o157 H7 strain TW10916"	"characteristics_ch1.1"
"replicate: 1"	"characteristics_ch1.2"
"strain: e. coli o157 H7 strain TW10948"	"characteristics_ch2.1"
"replicate: 3"	"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 as fixed factors. The linear model tested was Y (intensity) = array + dye + strain (clinical or bovine-biased)+ sample (biological replicate) + error. Significant differences in expression due to strain 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). SAM provided by TMEV was also used for data analysis."	"data_processing.1"
"5 ml of the culture was mixed with 1/10V 10% phenol:ethanol buffer to stabilize the RNA, and centrifuged at 4 oC, 4300 × g for 30 min to pellet cells.  The supernatant was decanted and cell pellets were suspended in 5 ml of buffer (2 mM EDTA, 20 mM NaOAc, pH 5.2) before mixing with equal volume of hot acid-phenol:chloroform (pH 4.5 with Iso Amyl Alcohol (IAA), 125:25:1) (Ambion, Austin, TX) and incubating at 65 oC with periodic shaking for 10 min.  The samples were centrifuged at 3220 × g for 20 min and the supernatant was subjected to further extractions with phenol:chloroform and chloroform:IAA (3).  RNA was precipitated overnight at -70 oC in 2.5 volume 100% ethanol and 1/10 volume 3 M sodium acetate pH 5.2.  RNA purification and DNase treatment of RNA samples were done with the Rneasy kit (Qiagen, Valencia, CA) and RNA quality was assessed on a formaldehyde-agarose gel."	"extract_protocol_ch1.1"
"5 ml of the culture was mixed with 1/10V 10% phenol:ethanol buffer to stabilize the RNA, and centrifuged at 4 oC, 4300 × g for 30 min to pellet cells.  The supernatant was decanted and cell pellets were suspended in 5 ml of buffer (2 mM EDTA, 20 mM NaOAc, pH 5.2) before mixing with equal volume of hot acid-phenol:chloroform (pH 4.5 with Iso Amyl Alcohol (IAA), 125:25:1) (Ambion, Austin, TX) and incubating at 65 oC with periodic shaking for 10 min.  The samples were centrifuged at 3220 × g for 20 min and the supernatant was subjected to further extractions with phenol:chloroform and chloroform:IAA (3).  RNA was precipitated overnight at -70 oC in 2.5 volume 100% ethanol and 1/10 volume 3 M sodium acetate pH 5.2.  RNA purification and DNase treatment of RNA samples were done with the Rneasy kit (Qiagen, Valencia, CA) and RNA quality was assessed on a formaldehyde-agarose gel."	"extract_protocol_ch2.1"
"TW10916 cells were grown in DMEM medium upto exponential phase (OD600~0.5, 2.5 h after inoclulation) at 37C."	"growth_protocol_ch1.1"
"TW10948 cells were grown in DMEM medium upto exponential phase (OD600~0.5, 2.5 h after inoclulation) at 37C."	"growth_protocol_ch2.1"
"Escherichia coli"	"organism_ch1.1"
"Escherichia coli"	"organism_ch2.1"
"clinical-1 strain grown to exponential phase of growth"	"source_name_ch1.1"
"bovine-biased-3 strain grown to exponential phase of growth"	"source_name_ch2.1"
"Clinical-1 vs Bovine-biased-3"	"title.1"
"strain: e. coli o157 H7 strain TW10916"	"characteristics_ch1.1"
"replicate: 1"	"characteristics_ch1.2"
"strain: e. coli o157 H7 strain TW10948"	"characteristics_ch2.1"
"replicate: 3"	"characteristics_ch2.2"
"TW10916 cells were grown in DMEM medium upto exponential phase (OD600~0.5, 2.5 h after inoclulation) at 37C."	"growth_protocol_ch1.1"
"TW10948 cells were grown in DMEM medium upto exponential phase (OD600~0.5, 2.5 h after inoclulation) at 37C."	"growth_protocol_ch2.1"
"Escherichia coli"	"organism_ch1.1"
"Escherichia coli"	"organism_ch2.1"
"clinical-1 strain grown to exponential phase of growth"	"source_name_ch1.1"
"bovine-biased-3 strain grown to exponential phase of growth"	"source_name_ch2.1"