"pooled RNA from all conditions including the control, reference"	"characteristics_ch1.1"
"BC-9ppm replicate 1"	"characteristics_ch2.1"
"The fluorescent spot intensities were quantified using ImaGeneÔ 5.6.1 (BioDiscovery Inc.) software. Background subtraction and normalization (LOWESS) was performed in GeneSpringä 7 (Silicon Genetics). (A lowess curve was fit to the log-intensity versus log-ratio plot. 20% of the data was used to calculate the lowess fit at each point. The curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then the value was set to 10). Only data from spots representing E. coli K-12 MG1655 genes were analyzed in our studies. All analyses were based on 3 biological replicates with the exception of the second biological replicate from conditions HCl and NaOH. These two observations were removed due to bad hybridization giving a total of 34 array hybridizations (observations). Genes not present in any of the 34 observations were filtered out, resulting in the analysis of 4279 out of 4289 MG1655 genes on the array. Missing values (data points) were replaced by using the KNNimpute procedure (k=10) on log2 transformed data."	"data_processing.1"
"Total RNA was extracted from 1 ml cells using the RNeasy Protect Bacteria Mini Prep kit (Qiagen) as recommended by the manufacturer including the “on-column” DNase treatment."	"extract_protocol_ch1.1"
"Total RNA was extracted from 1 ml cells using the RNeasy Protect Bacteria Mini Prep kit (Qiagen) as recommended by the manufacturer including the “on-column” DNase treatment."	"extract_protocol_ch2.1"
"The cultures were prepared by inoculating one colony from tryptone soya agar (TSA) (Oxoid) (overnight growth at 37°C) to 5 ml TSB and incubating overnight at 37°C, with shaking (200 rpm). This culture was initially diluted 1:10 in medium and used to inoculate room-temperature TSB for each of the different stress factors (40 ml total volume) to a final concentration of approx. 1´107 CFU/ml (1:100 dilution of overnight culture). For cold stress experiment the medium was chilled to 15°C prior to inoculation. The cultures were incubated at 37°C (except fpr 15°C and 46°C conditions), shaking at 200 rpm and samples were collected during exponential growth at a cell density of approx. 1´108 CFU/ml. All the stress conditions, including the control, were inoculated with the same overnight culture and started at the same time point. The experiment was performed 3 times at different days and with freshly prepared solutions, resulting in 3 biological replicates."	"growth_protocol_ch1.1"
"The cultures were prepared by inoculating one colony from tryptone soya agar (TSA) (Oxoid) (overnight growth at 37°C) to 5 ml TSB and incubating overnight at 37°C, with shaking (200 rpm). This culture was initially diluted 1:10 in medium and used to inoculate room-temperature TSB for each of the different stress factors (40 ml total volume) to a final concentration of approx. 1´107 CFU/ml (1:100 dilution of overnight culture). For cold stress experiment the medium was chilled to 15°C prior to inoculation. The cultures were incubated at 37°C (except fpr 15°C and 46°C conditions), shaking at 200 rpm and samples were collected during exponential growth at a cell density of approx. 1´108 CFU/ml. All the stress conditions, including the control, were inoculated with the same overnight culture and started at the same time point. The experiment was performed 3 times at different days and with freshly prepared solutions, resulting in 3 biological replicates."	"growth_protocol_ch2.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch2.1"
"pooled RNA from all conditions including the control, reference"	"source_name_ch1.1"
"BC-9ppm replicate 1"	"source_name_ch2.1"
"BC-9ppm replicate 1"	"title.1"
"CH3COOH (pH 5.9 ± 0.05); HCl (pH 4.75 ± 0.05); NaOH (pH 9.6 ± 0.05); EtOH (5%); NaCl (4.5%); Glycerol (15%); BC (7 and 9 mg/ml); EtBr (150 mg/ml); 46°C; 15°C"	"treatment_protocol_ch1.1"
"CH3COOH (pH 5.9 ± 0.05); HCl (pH 4.75 ± 0.05); NaOH (pH 9.6 ± 0.05); EtOH (5%); NaCl (4.5%); Glycerol (15%); BC (7 and 9 mg/ml); EtBr (150 mg/ml); 46°C; 15°C"	"treatment_protocol_ch2.1"
"pooled RNA from all conditions including the control, reference"	"characteristics_ch1.1"
"BC-9ppm replicate 1"	"characteristics_ch2.1"
"The cultures were prepared by inoculating one colony from tryptone soya agar (TSA) (Oxoid) (overnight growth at 37°C) to 5 ml TSB and incubating overnight at 37°C, with shaking (200 rpm). This culture was initially diluted 1:10 in medium and used to inoculate room-temperature TSB for each of the different stress factors (40 ml total volume) to a final concentration of approx. 1´107 CFU/ml (1:100 dilution of overnight culture). For cold stress experiment the medium was chilled to 15°C prior to inoculation. The cultures were incubated at 37°C (except fpr 15°C and 46°C conditions), shaking at 200 rpm and samples were collected during exponential growth at a cell density of approx. 1´108 CFU/ml. All the stress conditions, including the control, were inoculated with the same overnight culture and started at the same time point. The experiment was performed 3 times at different days and with freshly prepared solutions, resulting in 3 biological replicates."	"growth_protocol_ch1.1"
"The cultures were prepared by inoculating one colony from tryptone soya agar (TSA) (Oxoid) (overnight growth at 37°C) to 5 ml TSB and incubating overnight at 37°C, with shaking (200 rpm). This culture was initially diluted 1:10 in medium and used to inoculate room-temperature TSB for each of the different stress factors (40 ml total volume) to a final concentration of approx. 1´107 CFU/ml (1:100 dilution of overnight culture). For cold stress experiment the medium was chilled to 15°C prior to inoculation. The cultures were incubated at 37°C (except fpr 15°C and 46°C conditions), shaking at 200 rpm and samples were collected during exponential growth at a cell density of approx. 1´108 CFU/ml. All the stress conditions, including the control, were inoculated with the same overnight culture and started at the same time point. The experiment was performed 3 times at different days and with freshly prepared solutions, resulting in 3 biological replicates."	"growth_protocol_ch2.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch2.1"
"pooled RNA from all conditions including the control, reference"	"source_name_ch1.1"
"BC-9ppm replicate 1"	"source_name_ch2.1"
"CH3COOH (pH 5.9 ± 0.05); HCl (pH 4.75 ± 0.05); NaOH (pH 9.6 ± 0.05); EtOH (5%); NaCl (4.5%); Glycerol (15%); BC (7 and 9 mg/ml); EtBr (150 mg/ml); 46°C; 15°C"	"treatment_protocol_ch1.1"
"CH3COOH (pH 5.9 ± 0.05); HCl (pH 4.75 ± 0.05); NaOH (pH 9.6 ± 0.05); EtOH (5%); NaCl (4.5%); Glycerol (15%); BC (7 and 9 mg/ml); EtBr (150 mg/ml); 46°C; 15°C"	"treatment_protocol_ch2.1"