"strain: MG1655"	"characteristics_ch1.1"
"Data was obtained using the GeneChip® Command Console and Expression Console Software (AGCC; Version 3.2 and Expression Console; Version 1.2) using the MAS5 algorithm to generate .CHP files."	"data_processing.1"
"At each time point, 15 ml of each culture was mixed with 30 ml of RNAprotect Bacteria Reagent (Qiagen), vortexed for 5s, incubated for 5 min at room temperature, and centrifuged for 10 min at 5000g.  The pellet was processed using a Qiagen RNeasy Midi kit with on-column DNase digestion using Qiagen DNase.  The final elution of RNA from the column was with 160 μl RNase-free water."	"extract_protocol_ch1.1"
"The strains were grown exponentially (after initiation by a 1,000-fold dilution from overnight cultures) for ~5 generations at 37°C in Vogel-Bonner (VB) minimal medium supplemented with glucose (0.4%), pantothenic acid (5 µg/ml), casamino acids (Becton-Dickenson) (1%), and hypoxanthine (50 µg/ml)."	"growth_protocol_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"gpt strain w/o hypoxanthine 45 min at low dilution protocol"	"source_name_ch1.1"
"gpt_45 (Low Dilution) Rep3"	"title.1"
"At OD630nm = 0.1, the cultures were filtered through 47-mm diameter polycarbonate membrane filter (0.4 µm pore size; Millipore), washed with the same medium without hypoxanthine (Hx), and then resuspended at the same cell density (OD630 = 0.1) in the medium without Hx, and growth was continued as before.  The OD630 was followed closely during the next two hours, and the cells were periodically diluted with fresh, pre-warmed medium without Hx to keep OD between values 0.1 and 0.3 (low-dilution protocol).  Samples were taken for microarray analysis (see below) at 0, 15, 30, 45, 60 and 120 minutes.  In a parallel procedure, the optA1 gpt double mutant was also followed in a near-identical manner using a more highly diluted culture over a six-hour incubation period in the absence of hypoxanthine (high-dilution protocol).  The effectiveness of the latter treatment was followed microscopically by observing the extensive cellular filamentation associated with dGTP starvation."	"treatment_protocol_ch1.1"
"strain: MG1655"	"characteristics_ch1.1"
"The strains were grown exponentially (after initiation by a 1,000-fold dilution from overnight cultures) for ~5 generations at 37°C in Vogel-Bonner (VB) minimal medium supplemented with glucose (0.4%), pantothenic acid (5 µg/ml), casamino acids (Becton-Dickenson) (1%), and hypoxanthine (50 µg/ml)."	"growth_protocol_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"gpt strain w/o hypoxanthine 45 min at low dilution protocol"	"source_name_ch1.1"
"At OD630nm = 0.1, the cultures were filtered through 47-mm diameter polycarbonate membrane filter (0.4 µm pore size; Millipore), washed with the same medium without hypoxanthine (Hx), and then resuspended at the same cell density (OD630 = 0.1) in the medium without Hx, and growth was continued as before.  The OD630 was followed closely during the next two hours, and the cells were periodically diluted with fresh, pre-warmed medium without Hx to keep OD between values 0.1 and 0.3 (low-dilution protocol).  Samples were taken for microarray analysis (see below) at 0, 15, 30, 45, 60 and 120 minutes.  In a parallel procedure, the optA1 gpt double mutant was also followed in a near-identical manner using a more highly diluted culture over a six-hour incubation period in the absence of hypoxanthine (high-dilution protocol).  The effectiveness of the latter treatment was followed microscopically by observing the extensive cellular filamentation associated with dGTP starvation."	"treatment_protocol_ch1.1"