"Strain: Escherichia coli W3110 [F– IN(rrnD-rrnE)1]"	"characteristics_ch1.1"
"GCOS 1.0"	"data_processing.1"
"Samples for microarray analysis were collected as described earlier [1], (Samples were shortly mixed by vortexing, divided in 0.5 mL aliquots and 1. centrifuged for 3 min at 16,100 ×g and +4 °C. The pellets were resuspended in 250 µL of RNALater (Ambion, USA) and stored at -20 °C until analysis. RNA was extracted using the total RNA kit (A&A Biotechnology, Poland) ."	"extract_protocol_ch1.1"
"References"	"extract_protocol_ch1.2"
"1.	Neubauer, A., J. Soini, M. Bollok, M. Zenker, J. Sandqvist, J. Myllyharju, and P. Neubauer. 2007. Fermentation process for tetrameric human collagen prolyl 4-hydroxylase in Escherichia coli: improvement by gene optimisation of the PDI/beta subunit and repeated addition of the inducer anhydrotetracycline. J Biotechnol 128:308-321."	"extract_protocol_ch1.3"
"The cultivations were performed in a Biostat C 15 L bioreactor with the DCU-3 controlling unit and MFCS-win supervisory system (Sartorius) with an initial working volume of 8 L. The mineral salt medium contained per liter: 14.6 g K2HPO4, 3.6 g NaH2PO4 × 2 H2O, 2.0 g Na2SO4, 2.47 g (NH4)2SO4, 0.5 g NH4Cl, 1.0 g (NH4)2-H-citrate, 2 mM MgSO4, 0.1 g thiamine hydrochloride, 0.1 mL antifoam 204 (Sigma) and 2 mL trace element solution (1). The initial glucose concentration was 40 g L-1. The feed solution contained 650 g L-1 glucose. 2 mL L-1 of sterile filtered 1M MgSO4 were added regularly per OD600=10 increase."	"growth_protocol_ch1.1"
"Two precultures were performed in LB medium and mineral salt medium with 10 g L 1 of glucose without antifoam agent consecutively at 37 °C at a rotary shaker at 180 rpm. Main cultivations were started as batch cultures at a temperature of 37 °C. The pH was kept at 7.0 by controlled addition of 25% ammonia solution. At the end of the exponential growth phase (cell dry weight about 16 g L-1) the stirrer rate was lowered from 1000 rpm to 500 rpm, to provoke oxygen limitation by decreased oxygen transfer. Constant glucose feed of 100 g L-1 h-1 was started 15 min after the oxygen drop which was enough to ensure glucose excess during the whole cultivation."	"growth_protocol_ch1.2"
"References:"	"growth_protocol_ch1.3"
"1.Holme T, Arvidson S, Lindholm B, and Pavlu B. 1970. Enzymes: Laboratory-scale production. Process Biochemistry 62-66."	"growth_protocol_ch1.4"
"Escherichia coli"	"organism_ch1.1"
"E.coli W3110, fermentation sample taken 45 minutes after oxygen downshift"	"source_name_ch1.1"
"E.coli W3110, 45 minutes after oxygen downshift, sample S3"	"title.1"
"Strain: Escherichia coli W3110 [F– IN(rrnD-rrnE)1]"	"characteristics_ch1.1"
"The cultivations were performed in a Biostat C 15 L bioreactor with the DCU-3 controlling unit and MFCS-win supervisory system (Sartorius) with an initial working volume of 8 L. The mineral salt medium contained per liter: 14.6 g K2HPO4, 3.6 g NaH2PO4 × 2 H2O, 2.0 g Na2SO4, 2.47 g (NH4)2SO4, 0.5 g NH4Cl, 1.0 g (NH4)2-H-citrate, 2 mM MgSO4, 0.1 g thiamine hydrochloride, 0.1 mL antifoam 204 (Sigma) and 2 mL trace element solution (1). The initial glucose concentration was 40 g L-1. The feed solution contained 650 g L-1 glucose. 2 mL L-1 of sterile filtered 1M MgSO4 were added regularly per OD600=10 increase."	"growth_protocol_ch1.1"
"Two precultures were performed in LB medium and mineral salt medium with 10 g L 1 of glucose without antifoam agent consecutively at 37 °C at a rotary shaker at 180 rpm. Main cultivations were started as batch cultures at a temperature of 37 °C. The pH was kept at 7.0 by controlled addition of 25% ammonia solution. At the end of the exponential growth phase (cell dry weight about 16 g L-1) the stirrer rate was lowered from 1000 rpm to 500 rpm, to provoke oxygen limitation by decreased oxygen transfer. Constant glucose feed of 100 g L-1 h-1 was started 15 min after the oxygen drop which was enough to ensure glucose excess during the whole cultivation."	"growth_protocol_ch1.2"
"References:"	"growth_protocol_ch1.3"
"1.Holme T, Arvidson S, Lindholm B, and Pavlu B. 1970. Enzymes: Laboratory-scale production. Process Biochemistry 62-66."	"growth_protocol_ch1.4"
"Escherichia coli"	"organism_ch1.1"
"E.coli W3110, fermentation sample taken 45 minutes after oxygen downshift"	"source_name_ch1.1"