"strain: k-12 MG1655 wild-type"	"characteristics_ch1.1"
"medium: Neidhardt's EZ Rich Defined Medium (Teknova, USA)"	"characteristics_ch1.2"
"od600: 0.4"	"characteristics_ch1.3"
"treatment: 0.5 mg/ml menadione"	"characteristics_ch1.4"
"strain: k-12 MG1655 wild-type"	"characteristics_ch2.1"
"medium: Neidhardt's EZ Rich Defined Medium (Teknova, USA)"	"characteristics_ch2.2"
"od600: 0.4"	"characteristics_ch2.3"
"GenePix software (Axon Instruments, Union City, CA) version 5.1 was used to process the scanned data and generate the gpr files."	"data_processing.1"
"An RNeasy kit (Qiagen Ltd) was used to extract the total RNA according to manufacturers’ instructions. Contaminating DNA was removed by using on-column DNase I digestion (Qiagen Ltd). The quality and quantity of the RNA preparations were determined with an Agilent 2100 Bioanalyzer by using the RNA 6000 nano assay Labchip (Agilent, Stockport, United Kingdom)."	"extract_protocol_ch1.1"
"An RNeasy kit (Qiagen Ltd) was used to extract the total RNA according to manufacturers’ instructions. Contaminating DNA was removed by using on-column DNase I digestion (Qiagen Ltd). The quality and quantity of the RNA preparations were determined with an Agilent 2100 Bioanalyzer by using the RNA 6000 nano assay Labchip (Agilent, Stockport, United Kingdom)."	"extract_protocol_ch2.1"
"Escherichia coli"	"organism_ch1.1"
"Escherichia coli"	"organism_ch2.1"
"Escherichia coli K-12 treated with menadione_rep#1"	"source_name_ch1.1"
"E. coli K-12 untreated (reference sample)_rep #1"	"source_name_ch2.1"
"Oxidative stress in E. coli K-12 #1"	"title.1"
"A 5ml overnight culture of MG1655 was grown in Neidhardt's EZ Rich Defined Medium for 18 h at 37C. The culture was diluted 1:100 into 50 ml of fresh, prewarmed Neidhardt's EZ Rich Defined Medium in a 125 ml Ehrlenmeyer flask and shaken at 37C, 150 rpm in a New Brunswick Shaking water bath until the culture density reached 0.4. Half of the culture was transferred to a second identical flask containing menadione bisulphite to a final concentration of 0.5 mg/ml (this sample). The flasks were shaken for a further 10 min before 2 volumes of RNAprotect (TM) (Qiagen Ltd) were added to stabilise the RNA. Three independent cultures were processed on different occasions to make the 3 replicates used in this study. "	"treatment_protocol_ch1.1"
"A 5ml overnight culture of MG1655 was grown in Neidhardt's EZ Rich Defined Medium for 18 h at 37C. The culture was diluted 1:100 into 50 ml of fresh, prewarmed Neidhardt's EZ Rich Defined Medium in a 125 ml Ehrlenmeyer flask and shaken at 37C, 150 rpm in a New Bruswick Shaking water bath until the culture density reached 0.4. Half of the culture was transferred to a second identical flask containing menadione bisulphite to a final concentration of 0.5 mg/ml. This sample corresponds to the culture that was not treated with menadione. The flasks were shaken for a further 10 min before 2 volumes of RNAprotect (TM) (Qiagen Ltd) were added to stabilise the RNA. Three independent cultures were processed on different occasions to make the 3 replicates used in this study. "	"treatment_protocol_ch2.1"
"strain: k-12 MG1655 wild-type"	"characteristics_ch1.1"
"medium: Neidhardt's EZ Rich Defined Medium (Teknova, USA)"	"characteristics_ch1.2"
"od600: 0.4"	"characteristics_ch1.3"
"treatment: 0.5 mg/ml menadione"	"characteristics_ch1.4"
"strain: k-12 MG1655 wild-type"	"characteristics_ch2.1"
"medium: Neidhardt's EZ Rich Defined Medium (Teknova, USA)"	"characteristics_ch2.2"
"od600: 0.4"	"characteristics_ch2.3"
"Escherichia coli"	"organism_ch1.1"
"Escherichia coli"	"organism_ch2.1"
"Escherichia coli K-12 treated with menadione_rep#1"	"source_name_ch1.1"
"E. coli K-12 untreated (reference sample)_rep #1"	"source_name_ch2.1"
"A 5ml overnight culture of MG1655 was grown in Neidhardt's EZ Rich Defined Medium for 18 h at 37C. The culture was diluted 1:100 into 50 ml of fresh, prewarmed Neidhardt's EZ Rich Defined Medium in a 125 ml Ehrlenmeyer flask and shaken at 37C, 150 rpm in a New Brunswick Shaking water bath until the culture density reached 0.4. Half of the culture was transferred to a second identical flask containing menadione bisulphite to a final concentration of 0.5 mg/ml (this sample). The flasks were shaken for a further 10 min before 2 volumes of RNAprotect (TM) (Qiagen Ltd) were added to stabilise the RNA. Three independent cultures were processed on different occasions to make the 3 replicates used in this study. "	"treatment_protocol_ch1.1"
"A 5ml overnight culture of MG1655 was grown in Neidhardt's EZ Rich Defined Medium for 18 h at 37C. The culture was diluted 1:100 into 50 ml of fresh, prewarmed Neidhardt's EZ Rich Defined Medium in a 125 ml Ehrlenmeyer flask and shaken at 37C, 150 rpm in a New Bruswick Shaking water bath until the culture density reached 0.4. Half of the culture was transferred to a second identical flask containing menadione bisulphite to a final concentration of 0.5 mg/ml. This sample corresponds to the culture that was not treated with menadione. The flasks were shaken for a further 10 min before 2 volumes of RNAprotect (TM) (Qiagen Ltd) were added to stabilise the RNA. Three independent cultures were processed on different occasions to make the 3 replicates used in this study. "	"treatment_protocol_ch2.1"