"E. coli K12 (W3110), fed-batch/linear feed, unlimited growth (batch) "	"characteristics_ch1.1"
"E. coli K12 (W3110), fed-batch/linear feed, glucose limitation, 30 min after depletion of extracellular acetate"	"characteristics_ch2.1"
"Raw data were created by analyzing 16-bit tiff files with the Scan Array Express imaging software (microarray analysis system, version 3.0.0.0016, PerkinElmer, Massachusetts, USA; adaptive treshold method, total normalization method)."	"data_processing.1"
"Adaptive threshold (quantitation method) uses the parameters of the spot diameter and background inner and outer dimensions to create a spot mask and background mask, then refines the mask on a pixel-by-pixel basis. Total (normalization method), uses the intensity of each spot in relation to all spots."	"data_processing.2"
"The VALUE data are normalized log2(test/ref) ratios which were normalized 'print-tip-loess' using the software R (R, 2005) and the Limma package included (Smyth, 2005). Additionally, spots, which were classified as not found by the image analysis software, were down weighted to 10%."	"data_processing.3"
"Total RNA from 8.1*10exp9 cells was isolated using the RNeasy Kit (Qiagen) according to the manufacturer’s protocol. On-column DNase digestion was performed (RNase free DNase set, Qiagen). RNA concentration and quality were assessed photometrically (Nanodrop ND 1000, NanoDrop Technologies, Inc., Delaware, USA), by formaldehyde gel electrophoresis and bioanalyzer analysis (RNA 6000 Nano LabChip Kit, Agilent Bioanalyzer 2100, Agilent Technologies, California, USA). Only RNA with 260 nm / 280 nm ratio of 1.8 - 2 as well as 260 nm / 230 nm ratio > 1.8 was used for precipitation. The RNA was precipitated and resolved at the final concentration of 6 µg / µl required for reverse transcription and labeling with fluorescent dyes. Total RNA isolate was mixed with 1/10 volume of NaCl solution (3 M) and 2 volumes of ethanol (100 %) and stored at -20 °C overnight. The samples were subsequently centrifuged (14000 rpm; 20800 g) and the supernatant was discarded. The RNA was washed with ethanol (70 %) and vacuum dried. 100 µg of RNA were used for reverse transcription."	"extract_protocol_ch1.1"
"Total RNA from 8.1*10exp9 cells was isolated using the RNeasy Kit (Qiagen) according to the manufacturer’s protocol. On-column DNase digestion was performed (RNase free DNase set, Qiagen). RNA concentration and quality were assessed photometrically (Nanodrop ND 1000, NanoDrop Technologies, Inc., Delaware, USA), by formaldehyde gel electrophoresis and bioanalyzer analysis (RNA 6000 Nano LabChip Kit, Agilent Bioanalyzer 2100, Agilent Technologies, California, USA). Only RNA with 260 nm / 280 nm ratio of 1.8 - 2 as well as 260 nm / 230 nm ratio > 1.8 was used for precipitation. The RNA was precipitated and resolved at the final concentration of 6 µg / µl required for reverse transcription and labeling with fluorescent dyes. Total RNA isolate was mixed with 1/10 volume of NaCl solution (3 M) and 2 volumes of ethanol (100 %) and stored at -20 °C overnight. The samples were subsequently centrifuged (14000 rpm; 20800 g) and the supernatant was discarded. The RNA was washed with ethanol (70 %) and vacuum dried. 100 µg of RNA were used for reverse transcription."	"extract_protocol_ch2.1"
"The fed-batch cultivations were carried out with the bacterial strain E. coli K-12 W3110 (DSM 5911, German Collection of Microorganisms and Cell Cultures) in a 30-l bioreactor (Bioengineering AG, Wald, Switzerland). Minimal medium supplemented with glucose as the carbon source was used. The batch medium (batch volume VR,0 =17 l) consisted of 8.8 g l−1 glucose•H2O, 2.0 g l−1 Na2SO4•10H2O, 2.68 g l−1 (NH4)2SO4, 1.0 g l−1 NH4Cl, 14.6 g l−1 K2HPO4, 4.02 g l−1 NaH2PO4•2H2O, 0.01 g l−1 thiamine HCl; 0.3mM CaCl2•2H2O, 2mM MgSO4•7H2O; 3ml l−1 of trace element solution (TES: 16.7 g l−1 FeCl3•6H2O, 20.1 g l−1"	"growth_protocol_ch1.1"
"Escherichia coli str. K-12 substr. W3110"	"organism_ch1.1"
"Escherichia coli str. K-12 substr. W3110"	"organism_ch2.1"
"E. coli, unlimited growth (batch) "	"source_name_ch1.1"
"E. coli, glucose limitation, 30 min after depletion of extracellular acetate"	"source_name_ch2.1"
"E.coli_RviaT3_SR3"	"title.1"
"The culture medium samples were withdrawn with a capillary sampling probe as developed by Theobald et al. (1997), however, without using membrane-covered glass tubes."	"treatment_protocol_ch1.1"
"The cell samples were collected directly into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany) to avoid RNA degradation. The samples were centrifuged according to the manufacturer’s protocol and frozen at - 80 °C until RNA isolation."	"treatment_protocol_ch1.2"
"Theobald, U., Mailinger,W., Baltes, M., Rizzi, M., Reuss, M., 1997. In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae. 1. Experimental observations. Biotechnol. Bioeng. 55, 305–316."	"treatment_protocol_ch1.3"
"E. coli K12 (W3110), fed-batch/linear feed, unlimited growth (batch) "	"characteristics_ch1.1"
"E. coli K12 (W3110), fed-batch/linear feed, glucose limitation, 30 min after depletion of extracellular acetate"	"characteristics_ch2.1"
"The fed-batch cultivations were carried out with the bacterial strain E. coli K-12 W3110 (DSM 5911, German Collection of Microorganisms and Cell Cultures) in a 30-l bioreactor (Bioengineering AG, Wald, Switzerland). Minimal medium supplemented with glucose as the carbon source was used. The batch medium (batch volume VR,0 =17 l) consisted of 8.8 g l−1 glucose•H2O, 2.0 g l−1 Na2SO4•10H2O, 2.68 g l−1 (NH4)2SO4, 1.0 g l−1 NH4Cl, 14.6 g l−1 K2HPO4, 4.02 g l−1 NaH2PO4•2H2O, 0.01 g l−1 thiamine HCl; 0.3mM CaCl2•2H2O, 2mM MgSO4•7H2O; 3ml l−1 of trace element solution (TES: 16.7 g l−1 FeCl3•6H2O, 20.1 g l−1"	"growth_protocol_ch1.1"
"Escherichia coli str. K-12 substr. W3110"	"organism_ch1.1"
"Escherichia coli str. K-12 substr. W3110"	"organism_ch2.1"
"E. coli, unlimited growth (batch) "	"source_name_ch1.1"
"E. coli, glucose limitation, 30 min after depletion of extracellular acetate"	"source_name_ch2.1"
"The culture medium samples were withdrawn with a capillary sampling probe as developed by Theobald et al. (1997), however, without using membrane-covered glass tubes."	"treatment_protocol_ch1.1"
"The cell samples were collected directly into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany) to avoid RNA degradation. The samples were centrifuged according to the manufacturer’s protocol and frozen at - 80 °C until RNA isolation."	"treatment_protocol_ch1.2"
"Theobald, U., Mailinger,W., Baltes, M., Rizzi, M., Reuss, M., 1997. In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae. 1. Experimental observations. Biotechnol. Bioeng. 55, 305–316."	"treatment_protocol_ch1.3"