"growth phase: stationary"	"characteristics_ch1.1"
"Affymetrix Microarray Suite/GCOS"	"data_processing.1"
"The RNeasy Mini Purification Kit (Qiagen; Valencia, CA) was used to extract total RNA from E. coli O157:H7 cultures.  RNAlater Stabilization Reagent (1.2 ml) (Qiagen; Valencia, CA) was combined with 0.6 ml E. coli O157:H7.  After 10 min at room temperature, the mixture was centrifuged at 8000 x g for 10 min under refrigeration.  The supernatant was decanted and the bacterial pellet was stored at -70°C until further processed (2-10 h)."	"extract_protocol_ch1.1"
"One hundred µl tris-EDTA buffer (10 mM Tris-Cl, 1 mM EDTA, ph 8.0; Promega; Madison, WI) containing lysozyme (3 mg/ml; Sigma-Aldrich; St. Louis, MO) was added to each cell pellet.  The pellet was thoroughly mixed and incubated at room temperature for 10 min.  Buffer RLT (350 µl) was combined with the tris-EDTA/lysozyme cell suspension to further lyse cells.  The total volume was combined with 250 µl of 200 proof ethanol (Aaper Alcohol; Shelbyville, KY) to solubilize the cell lysate, and the entire sample was transferred to the RNeasy Mini Spin Column in a collection tube and centrifuged at 8000 x g for 15 sec at room temperature.  The silica-based membrane efficiently binds up to 100 µg of RNA longer than 200 bases.  The collection tube and eluate were discarded, and the spin column was placed in a new collection tube.  Buffer RW1 (700 µl) was applied to the column, centrifuged, and flow-through was discarded as described previously.  Twice, 500 µl of buffer RPE was applied to the spin column allowing 5 min prior to centrifugation at 8000 x g for 15 sec.  The spin column was placed in a 1.5 ml collection tube that was used for long-term storage.  In order to elute RNA from the spin column, 30 µl RNase-free water was applied directly to the membrane and centrifuged at 8000 x g for 15 sec.  The RNA eluate was stored at -80°C until evaluated for quantity, quality, and purity."	"extract_protocol_ch1.2"
"Cells were incubated at 37C prior to extraction"	"growth_protocol_ch1.1"
"Escherichia coli O157:H7 str. EDL933"	"organism_ch1.1"
"0% sodiumbenzoate_0min"	"source_name_ch1.1"
"E.coliO157_0%sodiumbenzoate_0min_rep2"	"title.1"
"Stationary phase growth (24hr) ~8 log CFU/ml was centrifuged at 8000xg 4C and resuspended in Luria-Bertaini broth with no sodium benozate"	"treatment_protocol_ch1.1"
"growth phase: stationary"	"characteristics_ch1.1"
"Cells were incubated at 37C prior to extraction"	"growth_protocol_ch1.1"
"Escherichia coli O157:H7 str. EDL933"	"organism_ch1.1"
"0% sodiumbenzoate_0min"	"source_name_ch1.1"
"Stationary phase growth (24hr) ~8 log CFU/ml was centrifuged at 8000xg 4C and resuspended in Luria-Bertaini broth with no sodium benozate"	"treatment_protocol_ch1.1"