"MW30 (rpoS)"	"characteristics_ch1.1"
"exponential phase"	"characteristics_ch1.2"
"Affymetrix .CEL files data were normalized with dChip using the array of median brightness (BS). Model method:model-base expression; background substraction: Mismatch Probe (PM/MM difference)"	"data_processing.1"
"Seven mililiter of phenol/water were added before incubating 10 min at 67°C with occasional stirring. The samples were cooled on ice and spun 10 min at 5000 rpm at 4°C. The aqueous phase was separated and extracted again once the same way and then once with phenol/chloroform (v/v 1:1). One tenth of the volume of 4M NaCl and 2.5 volumes of cold ethanol were then added to the aqueous phase. The tubes were left at -20°C for two hours then spun at 8500rpm at 4°C. The pellet was washed with 70% ethanol, dried under vacuum and resuspened in 300l sterile water and transferred to an eppendord tube. An amount of 34.5l Qiagen RDD buffer and 9.37l of RNase free DNase I (Qiagen) were added. After 15min at room temperature, the tubes were mixed by inversion and deproteinized as shown above with 300l phenol/H2O at room temperature. The RNA was then precipitated with 37.5µl NaCl 4M and 823µl cold ethanol. After 2 hours at -20°C, the tubes were centrifuged 30min at 10,000G at 4°C, the pellets were then washed with 70% ethanol then dried under vacuum and resuspended in 60µl sterile water. The RNAs were stored at -20°C."	"extract_protocol_ch1.1"
"The five bacterial strains (JO2057, JO2081, JO2083, JO3020 and MW30) were grown in 100ml LB 0.5% NaCl, M9 minimal glucose or M9 minimal glycerol at 200 rpm in New Brunswick laboratory shaker in 2liter flasks. The typical doubling time, observed in exponential phase in LB, was 40min for JO2057, JO2081, JO2083, MW30 and 75 min for JO3020. After growth curve calibration, the various growth phase sample were collected at the following cell densities: exponential phase: OD600 0.6-0.7; transition: 2.2-2.5 and stationary: 4.6-4.8 (3.0 for hupAB)."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"MW30 (rpoS), LB, exponential phase"	"source_name_ch1.1"
"MW30 rpoS, LB, exponential phase"	"title.1"
"A culture volume of 7ml was mixed with the same volume of boiling 2% SDS, 4mM EDTA and heated at 100°C for 3 to 5 minutes then vortexed. At this stage, the extract was either processed further or stored at -20°C."	"treatment_protocol_ch1.1"
"MW30 (rpoS)"	"characteristics_ch1.1"
"exponential phase"	"characteristics_ch1.2"
"The five bacterial strains (JO2057, JO2081, JO2083, JO3020 and MW30) were grown in 100ml LB 0.5% NaCl, M9 minimal glucose or M9 minimal glycerol at 200 rpm in New Brunswick laboratory shaker in 2liter flasks. The typical doubling time, observed in exponential phase in LB, was 40min for JO2057, JO2081, JO2083, MW30 and 75 min for JO3020. After growth curve calibration, the various growth phase sample were collected at the following cell densities: exponential phase: OD600 0.6-0.7; transition: 2.2-2.5 and stationary: 4.6-4.8 (3.0 for hupAB)."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"MW30 (rpoS), LB, exponential phase"	"source_name_ch1.1"
"A culture volume of 7ml was mixed with the same volume of boiling 2% SDS, 4mM EDTA and heated at 100°C for 3 to 5 minutes then vortexed. At this stage, the extract was either processed further or stored at -20°C."	"treatment_protocol_ch1.1"