"MG1655"	"characteristics_ch1.1"
"Genomic DNA served as a universal reference"	"characteristics_ch1.2"
"MG1655"	"characteristics_ch2.1"
"Elements with poor spot morphology or exhibiting uneven hybridization caused by dust particles or scratches, were flagged manually and excluded from further analyses. After local background  subtraction and global normalization relative to the genomic DNA reference, duplicate measurements on the same array were averaged, yielding a single vector for each time-point across a perturbation. The data from all hybridizations were combined into a matrix and scaled relative to each other using quantile-normalization as implemented in the Matlab Bioinformatics  toolbox. Biological duplicates from all experiments were averaged, leading to a single set of time-series data for each perturbation. Seven time-points were assayed for each perturbation, corresponding to 0, 4, 8, 12, 20, 28, and 44 minutes post transition."	"data_processing.1"
"DNA extraction: Genomic DNA was isolated and purified according to standard procedures (Ausubel et al. 1994).  Genomic DNA was fragmented by nebulization as described by Girgis et al. PLoS Genetics 3(9): e154 (2007) and purified by phenol/chloroform extraction and ethanol precipitated."	"extract_protocol_ch1.1"
"RNA extraction: A hot-phenol procedure was used to extract total RNA. Cell pellets were lysed with 500 μl TE (pH8.0), 50 μl 10% SDS and lysozyme (0.5 mg/ml). Total RNA was extracted sequentially with phenol/chloroform (preheated to 640 C), followed by chloroform/isoamyl alcohol. RNA was precipitated with 1/10 volume of 3M NaOAc (pH 5.2) and 2 volumes of ethanol. After incubating overnight at –200 C, samples were spun down and pellets were washed with ice cold 70% ethanol (prepared with DEPC- H2O). RNA was resuspended in water, DNase treated (RQ1 RNase-free DNase/ Promega, WI) and purified using an RNeasy purification kit (Qiagen, CA)."	"extract_protocol_ch2.1"
"Bacteria were grown in batch or bioreactor vessels in M9 minimal media supplemented with 0.4% glucose."	"growth_protocol_ch1.1"
"Bacteria were grown in batch or bioreactor vessels in M9 minimal media supplemented with 0.4% glucose."	"growth_protocol_ch2.1"
"Escherichia coli K-12"	"organism_ch1.1"
"Escherichia coli K-12"	"organism_ch2.1"
"genomic DNA"	"source_name_ch1.1"
"oxygen down shift, 28min"	"source_name_ch2.1"
"oxygen_down_28min"	"title.1"
"Physiological perturbations were carried out under a controlled environment in the context of bioreactor (Bioflo 110, New Brunswick Scientific) growth. Thermoelectric sensors and heaters were used to shift temperature profiles between 250 C and 370 C, and polarographic dissolved oxygen sensors (Mettler Toledo) and nitrogen gas was used to rapidly change oxygen saturation between anaerobic (0% dissolved oxygen) and aerobic (16-21% dissolved oxygen) condition."	"treatment_protocol_ch1.1"
"Physiological perturbations were carried out under a controlled environment in the context of bioreactor (Bioflo 110, New Brunswick Scientific) growth. Thermoelectric sensors and heaters were used to shift temperature profiles between 250 C and 370 C, and polarographic dissolved oxygen sensors (Mettler Toledo) and nitrogen gas was used to rapidly change oxygen saturation between anaerobic (0% dissolved oxygen) and aerobic (16-21% dissolved oxygen) condition."	"treatment_protocol_ch2.1"
"MG1655"	"characteristics_ch1.1"
"Genomic DNA served as a universal reference"	"characteristics_ch1.2"
"MG1655"	"characteristics_ch2.1"
"Bacteria were grown in batch or bioreactor vessels in M9 minimal media supplemented with 0.4% glucose."	"growth_protocol_ch1.1"
"Bacteria were grown in batch or bioreactor vessels in M9 minimal media supplemented with 0.4% glucose."	"growth_protocol_ch2.1"
"Escherichia coli K-12"	"organism_ch1.1"
"Escherichia coli K-12"	"organism_ch2.1"
"genomic DNA"	"source_name_ch1.1"
"oxygen down shift, 28min"	"source_name_ch2.1"
"Physiological perturbations were carried out under a controlled environment in the context of bioreactor (Bioflo 110, New Brunswick Scientific) growth. Thermoelectric sensors and heaters were used to shift temperature profiles between 250 C and 370 C, and polarographic dissolved oxygen sensors (Mettler Toledo) and nitrogen gas was used to rapidly change oxygen saturation between anaerobic (0% dissolved oxygen) and aerobic (16-21% dissolved oxygen) condition."	"treatment_protocol_ch1.1"
"Physiological perturbations were carried out under a controlled environment in the context of bioreactor (Bioflo 110, New Brunswick Scientific) growth. Thermoelectric sensors and heaters were used to shift temperature profiles between 250 C and 370 C, and polarographic dissolved oxygen sensors (Mettler Toledo) and nitrogen gas was used to rapidly change oxygen saturation between anaerobic (0% dissolved oxygen) and aerobic (16-21% dissolved oxygen) condition."	"treatment_protocol_ch2.1"