"strain: MC1000"	"characteristics_ch1.1"
"oxygen regime: daily shift between shaking and static (no shaking) conditions"	"characteristics_ch1.2"
"population: 4"	"characteristics_ch1.3"
"morphology: c"	"characteristics_ch1.4"
"culture type: evolved"	"characteristics_ch1.5"
"strain: MC1000"	"characteristics_ch2.1"
"culture type: Ancestor"	"characteristics_ch2.2"
"Statistical analysis was performed using R Limma package (Linear Models for Microarrays Data)  (Smyth 2004), where the two microarrays per sample were normalized using lowess normalization method. Multiple-gene probes results were merged and normalized using the MA table conversion tool available on the MOLGEN Bioinformatics Server (http://server.molgenrug.nl/ - Molecular genetics, university of Groningen, the Netherlands)."	"data_processing.1"
"Cells of each evolved colony type were collected by centrifugation at 13,000 × g for 1 min at 4°C and were immediately used for total RNA isolation with NucleoSpin RNA II isolation kit (Macherey – Nagel, Biokè, Leiden, the Netherlands)."	"extract_protocol_ch1.1"
"Cells of each evolved colony type were collected by centrifugation at 13,000 × g for 1 min at 4°C and were immediately used for total RNA isolation with NucleoSpin RNA II isolation kit (Macherey – Nagel, Biokè, Leiden, the Netherlands)."	"extract_protocol_ch2.1"
"Growth curves of all selected evolved colony types and the ancestor were obtained by growing them under their evolved environmental conditions in LB medium until Log-phase. For this, optical density was recorded at 600nm at a value of 0.6 to 0.7."	"growth_protocol_ch1.1"
"Growth curves of all selected evolved colony types and the ancestor were obtained by growing them under their evolved environmental conditions in LB medium until Log-phase. For this, optical density was recorded at 600nm at a value of 0.6 to 0.7."	"growth_protocol_ch2.1"
"Escherichia coli"	"organism_ch1.1"
"Escherichia coli"	"organism_ch2.1"
"Pure culture in LB"	"source_name_ch1.1"
"Pure culture in LB"	"source_name_ch2.1"
"Treatment B Population 4 Colony c replica 1"	"title.1"
"strain: MC1000"	"characteristics_ch1.1"
"oxygen regime: daily shift between shaking and static (no shaking) conditions"	"characteristics_ch1.2"
"population: 4"	"characteristics_ch1.3"
"morphology: c"	"characteristics_ch1.4"
"culture type: evolved"	"characteristics_ch1.5"
"strain: MC1000"	"characteristics_ch2.1"
"culture type: Ancestor"	"characteristics_ch2.2"
"Growth curves of all selected evolved colony types and the ancestor were obtained by growing them under their evolved environmental conditions in LB medium until Log-phase. For this, optical density was recorded at 600nm at a value of 0.6 to 0.7."	"growth_protocol_ch1.1"
"Growth curves of all selected evolved colony types and the ancestor were obtained by growing them under their evolved environmental conditions in LB medium until Log-phase. For this, optical density was recorded at 600nm at a value of 0.6 to 0.7."	"growth_protocol_ch2.1"
"Escherichia coli"	"organism_ch1.1"
"Escherichia coli"	"organism_ch2.1"
"Pure culture in LB"	"source_name_ch1.1"
"Pure culture in LB"	"source_name_ch2.1"