"genotype/variation: wild type"	"characteristics_ch1.1"
"culture condition: nitrate respiratory condition"	"characteristics_ch1.2"
"Raw CEL files were analyzed using robust multi-array average for normalization and calculation of probe intensities. The processed probe signals derived from each microarray were averaged for both the wild type and deletion mutant strains. This was done using the GCRMA package (version 2.13) from Bioconductor in R."	"data_processing.1"
"Samples for transcriptome analysis were taken from exponentially growing cells. From the cells treated by RNAprotect Bacteria Reagent (Qiagen), total RNA samples were isolated using RNeasy columns (Qiagen) in accordance with manufacturer’s instruction."	"extract_protocol_ch1.1"
"All strains used in this study were E. coli K-12 MG1655 and its derivatives. The deletion mutants (Δfnr and ΔarcA) were constructed by a λ red and FLP-mediated site-specific recombination method. Glycerol stocks of E. coli strains were inoculated into M9 minimal medium containing 0.2% (w/v) carbon source (glucose) and 0.1% (w/v) nitrogen source (NH4Cl), and cultured overnight at 37 °C with constant agitation. The cultures were diluted 1:100 into fresh minimal medium and then cultured at 37 °C to an appropriate cell density with constant agitation. For the anaerobic cultures, the minimal medium were flushed with nitrogen and then continuously monitored using a polarographic-dissolved oxygen probe (Cole-Parmer Instruments) to ensure anaerobicity. For nitrate respiration 20 mmol potassium nitrate was added."	"growth_protocol_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"affyexp_wt_glucose_NH4Cl_NO3"	"source_name_ch1.1"
"affyexp_wt_glucose_NH4Cl_NO3_2.CEL"	"title.1"
"genotype/variation: wild type"	"characteristics_ch1.1"
"culture condition: nitrate respiratory condition"	"characteristics_ch1.2"
"All strains used in this study were E. coli K-12 MG1655 and its derivatives. The deletion mutants (Δfnr and ΔarcA) were constructed by a λ red and FLP-mediated site-specific recombination method. Glycerol stocks of E. coli strains were inoculated into M9 minimal medium containing 0.2% (w/v) carbon source (glucose) and 0.1% (w/v) nitrogen source (NH4Cl), and cultured overnight at 37 °C with constant agitation. The cultures were diluted 1:100 into fresh minimal medium and then cultured at 37 °C to an appropriate cell density with constant agitation. For the anaerobic cultures, the minimal medium were flushed with nitrogen and then continuously monitored using a polarographic-dissolved oxygen probe (Cole-Parmer Instruments) to ensure anaerobicity. For nitrate respiration 20 mmol potassium nitrate was added."	"growth_protocol_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"affyexp_wt_glucose_NH4Cl_NO3"	"source_name_ch1.1"