"genotype/variation: EDL 933"	"characteristics_ch1.1"
"strain: O157: H7"	"characteristics_ch1.2"
"treatment: grown in lettuce rhizosphere"	"characteristics_ch1.3"
"genotype/variation: EDL 933"	"characteristics_ch2.1"
"strain: O157: H7"	"characteristics_ch2.2"
"treatment: grown without lettuce rhizosphere"	"characteristics_ch2.3"
"Signal intensities were normalized for spot and slide abnormalities with the spatial Lowess algorithm and analyzed by mixed-effect ANOVA (MAANOVA) (Kerr et al. 2000). Both Lowess and MAANOVA are part of the R/MAANOVA microarray statistical package, available at (http://www.jax.org/staff/churchill/labsite/). The resulting variety-by-gene interaction (VG) values of the control and experimental spot intensities were combined with the residual noise from each spot to obtain the filtered and adjusted expression values (Cui. et. al). Duplicate expression values from each array were combined, averaged and values from MAANOVA were subsequently subjected to significance analysis of microarray (SAM) data with the SAM package (Tusher. et.al). Significantly up- and down-regulated genes were identified based on a 1.5 cutoff threshold, a global false discovery rate lower than 5% (p<0.05). Six arrays representing a total of 12 replicates were analyzed between a treatment and a control."	"data_processing.1"
"Standard hot-phenol method"	"extract_protocol_ch1.1"
"Standard hot-phenol method"	"extract_protocol_ch2.1"
"Escherichia coli EDL 933 were grown in 10 ml of LB medium until stationary phase, collected by centrifugation at 8,000 ×g for 10 min, and washed twice with sterilized, plant growth medium (Caspersen et al. 1999). The resultant cells were re-suspended in 10 ml of the same plant growth medium to a final concentration of approximately 10E9 cells/ml. Germinated lettuce seedlings  were each aseptically transferred into holes in the growth boxes filled with 300 ml of plant growth medium, and 3 ml washed bacterial suspension was added to provide approximately 10E7 cells/ml of growth medium. Seedling boxes were germinated for a week and  transferred to a plant growth chamber, and the aeration pump (Luft Pump; Oceanic systems Inc. Dallas, TX) was immediately started. Each pump supplied aeration of three growth boxes, at a rate of 1.3 L /min. The seedling boxes were incubated under 80% RH at 25°C with a photoperiod of 16 h for 3 days"	"growth_protocol_ch1.1"
"Escherichia coli EDL 933 were grown in 10 ml of LB medium until stationary phase, collected by centrifugation at 8,000 ×g for 10 min, and washed twice with sterilized, plant growth medium (Caspersen et al. 1999). The resultant cells were re-suspended in 10 ml of the same plant growth medium to a final concentration of approximately 10E9 cells/ml. Germinated lettuce seedlings  were each aseptically transferred into holes in the growth boxes filled with 300 ml of plant growth medium, and 3 ml washed bacterial suspension was added to provide approximately 10E7 cells/ml of growth medium. Seedling boxes were germinated for a week and  transferred to a plant growth chamber, and the aeration pump (Luft Pump; Oceanic systems Inc. Dallas, TX) was immediately started. Each pump supplied aeration of three growth boxes, at a rate of 1.3 L /min. The seedling boxes were incubated under 80% RH at 25°C with a photoperiod of 16 h for 3 days"	"growth_protocol_ch2.1"
"Escherichia coli"	"organism_ch1.1"
"Escherichia coli"	"organism_ch2.1"
"Escherichia coli EDL 933 cells interacted with the lettuce rhizosphere for 3 days"	"source_name_ch1.1"
"Escherichia coli EDL 933 cells grown in the hydroponic system without interacting with the lettuce rhizosphere for 3 days"	"source_name_ch2.1"
"E. coli O157:H7 interacted with lettuce rhizosphere biological rep 3 slide 6"	"title.1"
"Following incubation, roots had been gently rinsed to remove loosely attached bacteria and roots were cut directly into 100 ml ice cold stop solution (5 % H2O-saturated phenol, pH 4.3, in 95% ethanol).  Root extracts were filtered using 0.5 µm filters to separate bacteria cells from plant cells in order to prevent interference of the cDNA labeling. Qiagen RNA protect solution was used to stabilize RNA during extraction. Bacteria had been collected by shaking and washing and stored in -80°C until using for RNA isolation."	"treatment_protocol_ch1.1"
"Following incubation, roots had been gently rinsed to remove loosely attached bacteria and roots were cut directly into 100 ml ice cold stop solution (5 % H2O-saturated phenol, pH 4.3, in 95% ethanol).  Root extracts were filtered using 0.5 µm filters to separate bacteria cells from plant cells in order to prevent interference of the cDNA labeling. Qiagen RNA protect solution was used to stabilize RNA during extraction. Bacteria had been collected by shaking and washing and stored in -80°C until using for RNA isolation."	"treatment_protocol_ch2.1"
"genotype/variation: EDL 933"	"characteristics_ch1.1"
"strain: O157: H7"	"characteristics_ch1.2"
"treatment: grown in lettuce rhizosphere"	"characteristics_ch1.3"
"genotype/variation: EDL 933"	"characteristics_ch2.1"
"strain: O157: H7"	"characteristics_ch2.2"
"treatment: grown without lettuce rhizosphere"	"characteristics_ch2.3"
"Escherichia coli EDL 933 were grown in 10 ml of LB medium until stationary phase, collected by centrifugation at 8,000 ×g for 10 min, and washed twice with sterilized, plant growth medium (Caspersen et al. 1999). The resultant cells were re-suspended in 10 ml of the same plant growth medium to a final concentration of approximately 10E9 cells/ml. Germinated lettuce seedlings  were each aseptically transferred into holes in the growth boxes filled with 300 ml of plant growth medium, and 3 ml washed bacterial suspension was added to provide approximately 10E7 cells/ml of growth medium. Seedling boxes were germinated for a week and  transferred to a plant growth chamber, and the aeration pump (Luft Pump; Oceanic systems Inc. Dallas, TX) was immediately started. Each pump supplied aeration of three growth boxes, at a rate of 1.3 L /min. The seedling boxes were incubated under 80% RH at 25°C with a photoperiod of 16 h for 3 days"	"growth_protocol_ch1.1"
"Escherichia coli EDL 933 were grown in 10 ml of LB medium until stationary phase, collected by centrifugation at 8,000 ×g for 10 min, and washed twice with sterilized, plant growth medium (Caspersen et al. 1999). The resultant cells were re-suspended in 10 ml of the same plant growth medium to a final concentration of approximately 10E9 cells/ml. Germinated lettuce seedlings  were each aseptically transferred into holes in the growth boxes filled with 300 ml of plant growth medium, and 3 ml washed bacterial suspension was added to provide approximately 10E7 cells/ml of growth medium. Seedling boxes were germinated for a week and  transferred to a plant growth chamber, and the aeration pump (Luft Pump; Oceanic systems Inc. Dallas, TX) was immediately started. Each pump supplied aeration of three growth boxes, at a rate of 1.3 L /min. The seedling boxes were incubated under 80% RH at 25°C with a photoperiod of 16 h for 3 days"	"growth_protocol_ch2.1"
"Escherichia coli"	"organism_ch1.1"
"Escherichia coli"	"organism_ch2.1"
"Escherichia coli EDL 933 cells interacted with the lettuce rhizosphere for 3 days"	"source_name_ch1.1"
"Escherichia coli EDL 933 cells grown in the hydroponic system without interacting with the lettuce rhizosphere for 3 days"	"source_name_ch2.1"
"Following incubation, roots had been gently rinsed to remove loosely attached bacteria and roots were cut directly into 100 ml ice cold stop solution (5 % H2O-saturated phenol, pH 4.3, in 95% ethanol).  Root extracts were filtered using 0.5 µm filters to separate bacteria cells from plant cells in order to prevent interference of the cDNA labeling. Qiagen RNA protect solution was used to stabilize RNA during extraction. Bacteria had been collected by shaking and washing and stored in -80°C until using for RNA isolation."	"treatment_protocol_ch1.1"
"Following incubation, roots had been gently rinsed to remove loosely attached bacteria and roots were cut directly into 100 ml ice cold stop solution (5 % H2O-saturated phenol, pH 4.3, in 95% ethanol).  Root extracts were filtered using 0.5 µm filters to separate bacteria cells from plant cells in order to prevent interference of the cDNA labeling. Qiagen RNA protect solution was used to stabilize RNA during extraction. Bacteria had been collected by shaking and washing and stored in -80°C until using for RNA isolation."	"treatment_protocol_ch2.1"