"strain: K-12"	"characteristics_ch1.1"
"substrain: DH1"	"characteristics_ch1.2"
"genotype/variation: DH1 (GB:AP012030)"	"characteristics_ch1.3"
"cell type: Original prototroph DH1 cells"	"characteristics_ch1.4"
"culture type: monoculture"	"characteristics_ch1.5"
"growth type: log phase"	"characteristics_ch1.6"
"Microarray data were processed using a custom R software for the finite hybridisation (FH) model (Ono et al., 2008, Bioinformatics 24, p1278)."	"data_processing.1"
"The processed gene expression data in log10 scale are provided in the supplementary file \"Ecoli_co_results.xlsx\"."	"data_processing.2"
"Metabolome data for these cultures are also provided in the supplementary file \"Ecoli_co_results.xlsx\", just for information."	"data_processing.3"
"The total RNA was extracted using an RNeasy kit, Qiagen, in accordance with the manufacturer's instructions."	"extract_protocol_ch1.1"
"All cultures were grown at 37C in well-mixed minimal media modified with M63 (mM63: pH 7.0, 62 mM K2HPO4, 39 mM KH2PO4, 15 mM ammonium sulfate, 1.8 µM FeSO4-7H2O, 15 µM thiamine hydrochloride, 0.2 mM MgSO4-7H2O and 22 mM glucose). One amino acid, Ile or Leu, was added to the monoculture medium when appropriate. Prior to coculturing, at both the initial inoculation and transfer, we washed the E. coli cells with fresh mM63 without amino acids to exclude the carry-over of supplements from the pre-culture. For coculture samples, we used cell culture inserts with a pore size of 0.45 µm at a density of 10^8/cm^2, and used six-well cell culture companion plates for the inserts (BD Falcon, Franklin Lakes, NJ, USA), to separately harvest I– and L– populations from cocultures (Hosoda et al., \"Transcriptome Analysis of a Microbial Coculture in which the Cell Populations Are Separated by a Membrane\", in Engineering and Analyzing Multicellular Systems (Methods in Molecular Biology), vol 1151, p151, 2014). We inoculated I– and L– cells at the initial concentration of 3x10^7 cells/mL and 6x10^5 cells/mL for the cocultures of ancestral (IA and LA) and evolved (IE and LE) cells, respectively, to adjust the late growth phase in one day. We incubated the coculture for 26 hours and then harvested the cells separately from the above and below the membrane insert. For monoculture samples, the required amino acid was supplied at 1mM, and 0.01mM for log-phase and starvation cells, respectively."	"growth_protocol_ch1.1"
"Escherichia coli K-12"	"organism_ch1.1"
"Original prototroph DH1 cells at log phase in monoculture"	"source_name_ch1.1"
"DH1-log"	"title.1"
"The cell cultures were interrupted by placing them directly into a cold phenol-ethanol solution (0.1g-phenol/mL-ethanol). The cells were collected using centrifugation at 12,000g for 5 min at 4C, and the pelleted cells were once stored at -80C prior to use."	"treatment_protocol_ch1.1"
"strain: K-12"	"characteristics_ch1.1"
"substrain: DH1"	"characteristics_ch1.2"
"genotype/variation: DH1 (GB:AP012030)"	"characteristics_ch1.3"
"cell type: Original prototroph DH1 cells"	"characteristics_ch1.4"
"culture type: monoculture"	"characteristics_ch1.5"
"growth type: log phase"	"characteristics_ch1.6"
"All cultures were grown at 37C in well-mixed minimal media modified with M63 (mM63: pH 7.0, 62 mM K2HPO4, 39 mM KH2PO4, 15 mM ammonium sulfate, 1.8 µM FeSO4-7H2O, 15 µM thiamine hydrochloride, 0.2 mM MgSO4-7H2O and 22 mM glucose). One amino acid, Ile or Leu, was added to the monoculture medium when appropriate. Prior to coculturing, at both the initial inoculation and transfer, we washed the E. coli cells with fresh mM63 without amino acids to exclude the carry-over of supplements from the pre-culture. For coculture samples, we used cell culture inserts with a pore size of 0.45 µm at a density of 10^8/cm^2, and used six-well cell culture companion plates for the inserts (BD Falcon, Franklin Lakes, NJ, USA), to separately harvest I– and L– populations from cocultures (Hosoda et al., \"Transcriptome Analysis of a Microbial Coculture in which the Cell Populations Are Separated by a Membrane\", in Engineering and Analyzing Multicellular Systems (Methods in Molecular Biology), vol 1151, p151, 2014). We inoculated I– and L– cells at the initial concentration of 3x10^7 cells/mL and 6x10^5 cells/mL for the cocultures of ancestral (IA and LA) and evolved (IE and LE) cells, respectively, to adjust the late growth phase in one day. We incubated the coculture for 26 hours and then harvested the cells separately from the above and below the membrane insert. For monoculture samples, the required amino acid was supplied at 1mM, and 0.01mM for log-phase and starvation cells, respectively."	"growth_protocol_ch1.1"
"Escherichia coli K-12"	"organism_ch1.1"
"Original prototroph DH1 cells at log phase in monoculture"	"source_name_ch1.1"
"The cell cultures were interrupted by placing them directly into a cold phenol-ethanol solution (0.1g-phenol/mL-ethanol). The cells were collected using centrifugation at 12,000g for 5 min at 4C, and the pelleted cells were once stored at -80C prior to use."	"treatment_protocol_ch1.1"