"strain: K12"	"characteristics_ch1.1"
"growth phase: Exponential"	"characteristics_ch1.2"
"strain: K12"	"characteristics_ch2.1"
"growth phase: exponential"	"characteristics_ch2.2"
"The data were normalised manually in Excel. For each spot, the median of the spot intensity minus the background were considered. Because we wanted to compare different environmental conditions, the cDNA signal in each condition was normalised to that of gDNA with M=ln(cDNA/gDNA). To ensure that the fluorescence measurements were independent of the overall signal intensity of the spot, the values of M were made independent of A=(lncDNA+lngDNA)/2 with a linear shift. Spots where the A values were less than 5.5 were not considered. Finally the experiments were aligned so that the median of M=0 and their deviation was normalised."	"data_processing.1"
"The analysis of the data is based on cross validation with datasets generated by Monte-Carlo simulation. The null hypothesis was that the gene expression changes monotonously as a function of NaCl concentration. The existence of a deviation from monotony was tested by F-tests for each gene probe. By comparing the number of probes with the lowest p(F) values for each NaCl concentrations with analogous results generated from Monte-Carlo sampling of the null hypothesis, we show that it is very unlikely that a switch between 4.5 and 5% NaCl could have happened by chance (in fact p<<0.01)."	"data_processing.2"
"Genomic DNA was purified from exponentially growing cells by lysis in lysozyme/mutanolysin, incubation in proteinase K/SDS, followed by a standard phenol/chloroform extraction procedure. Final pellets were dissolved in TE (10 mM Tris-HCl at pH 8.0, 1 mM EDTA). Genomic DNA was digested to completion with Sau3A1 (Promega) and purified by phenol/chloroform extraction. Synthesis and degradation of RNA were stopped by adding 1/4 volume of stop-solution (95% ethanol/5% phenol). Cells were harvested by centrifugation (4,000 rpm, 20 min) at 4°C and resuspended in 0.5 mL of  lysis buffer (0.5 mg/mL lysozyme, 10% SDS, Tris-EDTA buffer,  3 M sodium acetate, pH 5.2). Phenol (0.5 ml, pH 4.5) was added, and the samples were vortexed vigorously before incubation at 64 °C for 6 min. After placing the samples on ice, the aqueous layer was extracted with 1:1 phenol:chloroform and with chloroform, and the RNA was precipitated with ethanol at -80°C. After resuspension, RNA concentration and purity was assessed by NanoDrop ND-1000 UV spectrophotometer (Nanodrop Technologies, Wilmingon, DE) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), respectively."	"extract_protocol_ch1.1"
"Genomic DNA was purified from exponentially growing cells by lysis in lysozyme/mutanolysin, incubation in proteinase K/SDS, followed by a standard phenol/chloroform extraction procedure. Final pellets were dissolved in TE (10 mM Tris-HCl at pH 8.0, 1 mM EDTA). Genomic DNA was digested to completion with Sau3A1 (Promega) and purified by phenol/chloroform extraction. Synthesis and degradation of RNA were stopped by adding 1/4 volume of stop-solution (95% ethanol/5% phenol). Cells were harvested by centrifugation (4,000 rpm, 20 min) at 4°C and resuspended in 0.5 mL of  lysis buffer (0.5 mg/mL lysozyme, 10% SDS, Tris-EDTA buffer,  3 M sodium acetate, pH 5.2). Phenol (0.5 ml, pH 4.5) was added, and the samples were vortexed vigorously before incubation at 64 °C for 6 min. After placing the samples on ice, the aqueous layer was extracted with 1:1 phenol:chloroform and with chloroform, and the RNA was precipitated with ethanol at -80°C. After resuspension, RNA concentration and purity was assessed by NanoDrop ND-1000 UV spectrophotometer (Nanodrop Technologies, Wilmingon, DE) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), respectively."	"extract_protocol_ch2.1"
"E. coli was grown to exponential phase in glucose minimal medium in the presence of the osmoprotectant glycine beatine with a range of salt concentrations at 2, 3.5 (2 repeats), 4.5, 5 and 5.5% NaCl.  E. coli were inoculated at 104 cfu/ml and cultures incubated to reach 107 cfu/ml, an ODs of about 0.03 (cultures entered stationary phase at 108 cfu/ml)  before harvesting."	"growth_protocol_ch1.1"
"E. coli was grown to exponential phase in glucose minimal medium in the presence of the osmoprotectant glycine beatine with a range of salt concentrations at 2, 3.5 (2 repeats), 4.5, 5 and 5.5% NaCl.  E. coli were inoculated at 104 cfu/ml and cultures incubated to reach 107 cfu/ml, an ODs of about 0.03 (cultures entered stationary phase at 108 cfu/ml)  before harvesting."	"growth_protocol_ch2.1"
"Escherichia coli K-12"	"organism_ch1.1"
"Escherichia coli K-12"	"organism_ch2.1"
"E. coli, stressed by NaCl, in presence of glycine betaine"	"source_name_ch1.1"
"E. coli, stressed by NaCl, in presence of glycine betaine"	"source_name_ch2.1"
"E. coli 4.5% NaCl"	"title.1"
"strain: K12"	"characteristics_ch1.1"
"growth phase: Exponential"	"characteristics_ch1.2"
"strain: K12"	"characteristics_ch2.1"
"growth phase: exponential"	"characteristics_ch2.2"
"E. coli was grown to exponential phase in glucose minimal medium in the presence of the osmoprotectant glycine beatine with a range of salt concentrations at 2, 3.5 (2 repeats), 4.5, 5 and 5.5% NaCl.  E. coli were inoculated at 104 cfu/ml and cultures incubated to reach 107 cfu/ml, an ODs of about 0.03 (cultures entered stationary phase at 108 cfu/ml)  before harvesting."	"growth_protocol_ch1.1"
"E. coli was grown to exponential phase in glucose minimal medium in the presence of the osmoprotectant glycine beatine with a range of salt concentrations at 2, 3.5 (2 repeats), 4.5, 5 and 5.5% NaCl.  E. coli were inoculated at 104 cfu/ml and cultures incubated to reach 107 cfu/ml, an ODs of about 0.03 (cultures entered stationary phase at 108 cfu/ml)  before harvesting."	"growth_protocol_ch2.1"
"Escherichia coli K-12"	"organism_ch1.1"
"Escherichia coli K-12"	"organism_ch2.1"
"E. coli, stressed by NaCl, in presence of glycine betaine"	"source_name_ch1.1"
"E. coli, stressed by NaCl, in presence of glycine betaine"	"source_name_ch2.1"