"Strain: K-12 reduced genome"	"characteristics_ch1.1"
"Isolate: MDS42"	"characteristics_ch1.2"
"Growth phase: exponential"	"characteristics_ch1.3"
"Growth medium: MOPS minimal, 0.4% glucose, 0.5% casamino acids"	"characteristics_ch1.4"
"Culture conditions: 37 C with shaking at 220 RPM"	"characteristics_ch1.5"
"Drug: none"	"characteristics_ch1.6"
"Extraction: Rneasy"	"characteristics_ch1.7"
"Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the PLIER algorithm in the Affymetrix Expression Console. No further adjustments were made to the data in the table."	"data_processing.1"
"TRI Reagent (Sigma) or Rneasy (QIAGEN) according to manufacturer's protocol. No Rnase treatment."	"extract_protocol_ch1.1"
"Overnight culture in LB medium was innoculated from a single colony. The overnight culture was diluted 1/200 into MOPS minimal medium (Neidhardt, J. Bacteriol., 1974) and incubated with shaking at 37 C until OD600=0.5 or OD600=0.3. Total culture volume 10 ml."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Reduced genome strain MDS42, control sample, exponential phase"	"source_name_ch1.1"
"Coli-MDS42_no-drug_rep2"	"title.1"
"Bicyclomycin (BCM, gift of Schering-Plough Animal Health) was added to the culture at the indicated dose for 20 minutes. Culture was added to 2 volumes of RNAprotect Bacterial Reagent (QIAGEN)."	"treatment_protocol_ch1.1"
"Strain: K-12 reduced genome"	"characteristics_ch1.1"
"Isolate: MDS42"	"characteristics_ch1.2"
"Growth phase: exponential"	"characteristics_ch1.3"
"Growth medium: MOPS minimal, 0.4% glucose, 0.5% casamino acids"	"characteristics_ch1.4"
"Culture conditions: 37 C with shaking at 220 RPM"	"characteristics_ch1.5"
"Drug: none"	"characteristics_ch1.6"
"Extraction: Rneasy"	"characteristics_ch1.7"
"Overnight culture in LB medium was innoculated from a single colony. The overnight culture was diluted 1/200 into MOPS minimal medium (Neidhardt, J. Bacteriol., 1974) and incubated with shaking at 37 C until OD600=0.5 or OD600=0.3. Total culture volume 10 ml."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Reduced genome strain MDS42, control sample, exponential phase"	"source_name_ch1.1"
"Bicyclomycin (BCM, gift of Schering-Plough Animal Health) was added to the culture at the indicated dose for 20 minutes. Culture was added to 2 volumes of RNAprotect Bacterial Reagent (QIAGEN)."	"treatment_protocol_ch1.1"