"strain: EHEC strain"	"characteristics_ch1.1"
"referece: The three genomes contributing to the ORFs on the microarray."	"characteristics_ch2.1"
"Data obtained from E. coli O157:H7 microarrays were normalized using the Ratio-based and Lowess methods in Acuity 3.1 (Axon instruments) before analysis. The normalized data for all strains were converted into log2 (Fluor 647/Fluor 546) in Acuity 3.1 and subsequently analyzed in Microsoft Excel. Control, blank, and test spots with a mean intensity below that of the mean of all negative controls were removed from the analysis. The arithmetic mean of the remaining spots across the duplicates was taken to construct the dataset. GACK (Genomotyping Analysis by Charles Kim), was used to generate a cut off value determining the presence or absence of genes, and a dendrogram using the Euclidean distance metric with average linkage was created with tMEV v4.1."	"data_processing.1"
"The cultures were centrifuged at 8000 rpm for 10 minutes and the pellet was dissolved in 15 mL of 10 mM NaCl, 20 mM Tris-HCl (pH 8.0), 1 mM EDTA, 100 μg/mL proteinase K and 0.5% SDS. This suspension was incubated at 50oC for 2 h and DNA extracted with an equal volume of phenol:chloroform:isoamyl alcohol (25:24:1). Following centrifugation for 10 min at 8000 rpm, the upper phase was removed and precipitated by adding 0.1 volume of 3 M NaOAc (pH 5.2) and 2 volumes of 99% ethanol. The DNA precipitate was then spooled out of the solution using a sterile glass rod, washed with 70% ethanol, and dissolved in 5 mL of TE (10 mM Tris-HCl, 1 mM EDTA, pH 8.0) buffer."	"extract_protocol_ch1.1"
"The cultures were centrifuged at 8000 rpm for 10 minutes and the pellet was dissolved in 15 mL of 10 mM NaCl, 20 mM Tris-HCl (pH 8.0), 1 mM EDTA, 100 μg/mL proteinase K and 0.5% SDS. This suspension was incubated at 50oC for 2 h and DNA extracted with an equal volume of phenol:chloroform:isoamyl alcohol (25:24:1). Following centrifugation for 10 min at 8000 rpm, the upper phase was removed and precipitated by adding 0.1 volume of 3 M NaOAc (pH 5.2) and 2 volumes of 99% ethanol. The DNA precipitate was then spooled out of the solution using a sterile glass rod, washed with 70% ethanol, and dissolved in 5 mL of TE (10 mM Tris-HCl, 1 mM EDTA, pH 8.0) buffer."	"extract_protocol_ch2.1"
"See the paper Variation in the Genomic islands of porcine enteropathogenic Escherichia coli strains of serogroup O45 revealed by comparative genomic hybridization and PCR by Bruant and Zhang et al. 2009"	"growth_protocol_ch1.1"
"See the paper Variation in the Genomic islands of porcine enteropathogenic Escherichia coli strains of serogroup O45 revealed by comparative genomic hybridization and PCR by Bruant and Zhang et al. 2009"	"growth_protocol_ch2.1"
"Escherichia coli O157:H7"	"organism_ch1.1"
"Escherichia coli O157:H7 str. EDL933"	"organism_ch2.1"
"Escherichia coli O157:H7 str. Sakai"	"organism_ch2.2"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch2.3"
"Overnight bacterial culture in BHI broth."	"source_name_ch1.1"
"Overnight bacterial culture in BHI broth."	"source_name_ch2.1"
"EDL (O157:H7)"	"title.1"
"See the paper Variation in the Genomic islands of porcine enteropathogenic Escherichia coli strains of serogroup O45 revealed by comparative genomic hybridization and PCR by Bruant and Zhang et al. 2009"	"treatment_protocol_ch1.1"
"See the paper Variation in the Genomic islands of porcine enteropathogenic Escherichia coli strains of serogroup O45 revealed by comparative genomic hybridization and PCR by Bruant and Zhang et al. 2009"	"treatment_protocol_ch2.1"
"strain: EHEC strain"	"characteristics_ch1.1"
"referece: The three genomes contributing to the ORFs on the microarray."	"characteristics_ch2.1"
"See the paper Variation in the Genomic islands of porcine enteropathogenic Escherichia coli strains of serogroup O45 revealed by comparative genomic hybridization and PCR by Bruant and Zhang et al. 2009"	"growth_protocol_ch1.1"
"See the paper Variation in the Genomic islands of porcine enteropathogenic Escherichia coli strains of serogroup O45 revealed by comparative genomic hybridization and PCR by Bruant and Zhang et al. 2009"	"growth_protocol_ch2.1"
"Escherichia coli O157:H7"	"organism_ch1.1"
"Escherichia coli O157:H7 str. EDL933"	"organism_ch2.1"
"Escherichia coli O157:H7 str. Sakai"	"organism_ch2.2"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch2.3"
"Overnight bacterial culture in BHI broth."	"source_name_ch1.1"
"Overnight bacterial culture in BHI broth."	"source_name_ch2.1"
"See the paper Variation in the Genomic islands of porcine enteropathogenic Escherichia coli strains of serogroup O45 revealed by comparative genomic hybridization and PCR by Bruant and Zhang et al. 2009"	"treatment_protocol_ch1.1"
"See the paper Variation in the Genomic islands of porcine enteropathogenic Escherichia coli strains of serogroup O45 revealed by comparative genomic hybridization and PCR by Bruant and Zhang et al. 2009"	"treatment_protocol_ch2.1"