"A pool of 3 E. coli clones forming small colonies when plated on TTagar and derived from E. coli B REL606 after 150 days of seasonal evolution experiment in 18mm test tubes in DMga medium."	"characteristics_ch1.1"
"Ancestral E. coli B REL606 strain"	"characteristics_ch2.1"
"Statistical preprocessing steps were conducted with ArrayPipe (version 1.7), a web-based software designed for processing of microarray data (www.pathogenomics.ca/arraypipe, Hokamp et al. 2004). The following pre-processing steps were applied: 1) flagging of markers and control spots, 2) subgrid-wise background correction, using the median of the lower 10% foreground intensity as an estimate for the background noise, 3) data-shifting, 4) limma’s LOESS normalization by print tip, 5) merging of duplicate spots."	"data_processing.1"
"VALUEs are calculated as log2-transformed (test/ref) ratios after background correction and limma's LOESS normalization"	"data_processing.2"
"Total RNA was extracted using Qiagen RNeasy Mini Kit. DNA was removed using Ambion DNA-free kit. RNA quality was assessed using 2% agarose gels and OD260/OD280 ratio. Amino-allyl dUTP was used to label 5µg of RNA during reverse transcription. The reverse transcription was performed at 42°C during 50 min using 600 units of superscript RT II (Invitrogen), 3 µg of random hexamers, 0.6mM dATP, dCTP and dGTP, 0.2mM dTTP, and 0.4mM amino-allyl dUTP (Ambion). RNA was then degraded by incubation at 65°C, for 15 min, after adding 10µL of 0.5M EDTA and 10µL of 1M NaOH."	"extract_protocol_ch1.1"
"Total RNA was extracted using Qiagen RNeasy Mini Kit. DNA was removed using Ambion DNA-free kit. RNA quality was assessed using 2% agarose gels and OD260/OD280 ratio. Amino-allyl dUTP was used to label 5µg of RNA during reverse transcription. The reverse transcription was performed at 42°C during 50 min using 600 units of superscript RT II (Invitrogen), 3 µg of random hexamers, 0.6mM dATP, dCTP and dGTP, 0.2mM dTTP, and 0.4mM amino-allyl dUTP (Ambion). RNA was then degraded by incubation at 65°C, for 15 min, after adding 10µL of 0.5M EDTA and 10µL of 1M NaOH."	"extract_protocol_ch2.1"
"Frozen bacteria were grown overnight in 18mm test tubes containing DMga medium, 500µL of culture was transferred to 50mL of fresh DMga in 500mL flasks and grown for 18 hours 37°C, 250rpm. Extraction was performed just after."	"growth_protocol_ch1.1"
"Frozen bacteria were grown overnight in 18mm test tubes containing DMga medium, 500µL of culture was transferred to 50mL of fresh DMga in 500mL flasks and grown for 18hours 37°C, 250rpm. Extraction was performed just after."	"growth_protocol_ch2.1"
"Escherichia coli"	"organism_ch1.1"
"Escherichia coli"	"organism_ch2.1"
"S, TP4"	"source_name_ch1.1"
"A, TP4"	"source_name_ch2.1"
"SA_TP4_repl2"	"title.1"
"NA"	"treatment_protocol_ch1.1"
"NA"	"treatment_protocol_ch2.1"
"A pool of 3 E. coli clones forming small colonies when plated on TTagar and derived from E. coli B REL606 after 150 days of seasonal evolution experiment in 18mm test tubes in DMga medium."	"characteristics_ch1.1"
"Ancestral E. coli B REL606 strain"	"characteristics_ch2.1"
"Frozen bacteria were grown overnight in 18mm test tubes containing DMga medium, 500µL of culture was transferred to 50mL of fresh DMga in 500mL flasks and grown for 18 hours 37°C, 250rpm. Extraction was performed just after."	"growth_protocol_ch1.1"
"Frozen bacteria were grown overnight in 18mm test tubes containing DMga medium, 500µL of culture was transferred to 50mL of fresh DMga in 500mL flasks and grown for 18hours 37°C, 250rpm. Extraction was performed just after."	"growth_protocol_ch2.1"
"Escherichia coli"	"organism_ch1.1"
"Escherichia coli"	"organism_ch2.1"
"S, TP4"	"source_name_ch1.1"
"A, TP4"	"source_name_ch2.1"
"NA"	"treatment_protocol_ch1.1"
"NA"	"treatment_protocol_ch2.1"