"strain: strain K12 substrain MG1655"	"characteristics_ch1.1"
"growth protocol: Controls grown to an optimal temperature of 37°C"	"characteristics_ch1.2"
"growth phase: stationary phase (grown to an OD600nm of 0.9)"	"characteristics_ch1.3"
"strain: strain K12 substrain MG1655"	"characteristics_ch2.1"
"growth protocol: Treatment 4 (core temperature of 71°C)"	"characteristics_ch2.2"
"growth phase: stationary phase (grown to an OD600nm of 0.9)"	"characteristics_ch2.3"
"LOWESS normalized data obtained from log2 of processed Red signal (treated)/processed Green signal (control) are given in the data table below. All microarray data were analyzed using R software and Limma package (part of Bioconductor). All the probes encoding for positive and negative controls were not used and have been removed. Only raw data superior to background values and with homogeneous fluorescent signals were considered (H < 0.2). Red and green signal heterogeneity was estimated as followed: H = |(trimmed mean of raw intensity - median of raw intensity)|/|(0.5*(trimmed mean of raw intensity + median of raw intensity)). After LOWESS normalization, the differences between the four heat-treatments were tested by Analysis of Variance (ANOVA) followed by a priori tests (P-value < 0.0001 and P-value FDR after Benjamini Yekutieli adjustment < 0.01). Six contrasts (Contrast1:T1 vs T2, Contrast2:T1 vs T3, Contrast3: T1 vs T4, Contrast4: T2 vs T3, Contrast5: T2 vs T4, Contrast6: T3 vs T4) were performed. Normalized Log2 ratio between treatments and the results of the statistical analysis have been linked as a supplementary file on the Series record."	"data_processing.1"
"Frozen cell pellets were lyzed with lysozyme (Sigma Aldrich) and proteinase K (Qiagen Inc.) at room temperature. Total RNA was isolated from cell lysates using RNeasy Midi Kit according to the manufacturer's instructions (Qiagen Inc.). All RNA samples were then treated with DNase I (Ambion, Life technologies) before a phenol/chloroform purification and an overnight precipitation at -20°C in absolute ethanol containing LiCl 8M. After centrifugation, RNA pellets were air-dried in a vacuum concentrator ( vacufuge plus; Eppendorf)."	"extract_protocol_ch1.1"
"Frozen cell pellets were lyzed with lysozyme (Sigma Aldrich) and proteinase K (Qiagen Inc.) at room temperature. Total RNA was isolated from cell lysates using RNeasy Midi Kit according to the manufacturer's instructions (Qiagen Inc.). All RNA samples were then treated with DNase I (Ambion, Life technologies) before a phenol/chloroform purification and an overnight precipitation at -20°C in absolute ethanol containing LiCl 8M. After centrifugation, RNA pellets were air-dried in a vacuum concentrator ( vacufuge plus; Eppendorf)."	"extract_protocol_ch2.1"
"For each biological replicate, frozen aliquots (500μl) of E. coli K12 stock cultures were subcultured in 10 ml of Brain Heart Infusion (BHI) and incubated overnight at 37°C. Cells were then sub-cultured (1% v/v) into 50ml BHI broth and incubated at 37°C for 24h under constant agitation (150 rpm). The bacterial suspensions were then inoculated (1% v/v) in 200ml BHI broth and grown in the same conditions to stationary phase (OD600nm of 0.9)."	"growth_protocol_ch1.1"
"For each biological replicate, frozen aliquots (500μl) of E. coli K12 stock cultures were subcultured in 10 ml of Brain Heart Infusion (BHI) and incubated overnight at 37°C. Cells were then sub-cultured (1% v/v) into 50ml BHI broth and incubated at 37°C for 24h under constant agitation (150 rpm). The bacterial suspensions were then inoculated (1% v/v) in 200ml BHI broth and grown in the same conditions to stationary phase (OD600nm of 0.9)."	"growth_protocol_ch2.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch2.1"
"Control bacteria at 37°C (common reference).  Total RNA isolated from 5 indepedent cultures (pooled after cDNA labeling)."	"source_name_ch1.1"
"Bacteria at 71°C"	"source_name_ch2.1"
"Bacteria suspension heated to a core temperature of 71°C                - Replicate 1"	"title.1"
"After reaching an OD600nm of 0.9, cell cultures were placed immediately in a shaking water bath along with another BHI flask carrying a type T thermocouple connected to a MultiPaq 21 datalogger (Datapaq Inc.) for temperature profile and the process lethality values monitoring in real time. Bacteria suspension were heated at 58°C to process lethality values of 2 and 3, at 60°C to a process lethality value of 3, or until a temperature of 71°C was reached. Just after heating, cell suspension was cooled in an iced water bath under constant agitation (150 rpm) until the temperature dropped back to no less than 37°C in order to avoid cold stress. Cell suspensions were then centrifuged and the remaining cell pellets were treated with RNA protect bacteria reagent (Qiagen Inc.) prior to freezing at -80°C."	"treatment_protocol_ch1.1"
"After reaching an OD600nm of 0.9, cell cultures were placed immediately in a shaking water bath along with another BHI flask carrying a type T thermocouple connected to a MultiPaq 21 datalogger (Datapaq Inc.) for temperature profile and the process lethality values monitoring in real time. Bacteria suspension were heated at 58°C to process lethality values of 2 and 3, at 60°C to a process lethality value of 3, or until a temperature of 71°C was reached. Just after heating, cell suspension was cooled in an iced water bath under constant agitation (150 rpm) until the temperature dropped back to no less than 37°C in order to avoid cold stress. Cell suspensions were then centrifuged and the remaining cell pellets were treated with RNA protect bacteria reagent (Qiagen Inc.) prior to freezing at -80°C."	"treatment_protocol_ch2.1"
"strain: strain K12 substrain MG1655"	"characteristics_ch1.1"
"growth protocol: Controls grown to an optimal temperature of 37°C"	"characteristics_ch1.2"
"growth phase: stationary phase (grown to an OD600nm of 0.9)"	"characteristics_ch1.3"
"strain: strain K12 substrain MG1655"	"characteristics_ch2.1"
"growth protocol: Treatment 4 (core temperature of 71°C)"	"characteristics_ch2.2"
"growth phase: stationary phase (grown to an OD600nm of 0.9)"	"characteristics_ch2.3"
"For each biological replicate, frozen aliquots (500μl) of E. coli K12 stock cultures were subcultured in 10 ml of Brain Heart Infusion (BHI) and incubated overnight at 37°C. Cells were then sub-cultured (1% v/v) into 50ml BHI broth and incubated at 37°C for 24h under constant agitation (150 rpm). The bacterial suspensions were then inoculated (1% v/v) in 200ml BHI broth and grown in the same conditions to stationary phase (OD600nm of 0.9)."	"growth_protocol_ch1.1"
"For each biological replicate, frozen aliquots (500μl) of E. coli K12 stock cultures were subcultured in 10 ml of Brain Heart Infusion (BHI) and incubated overnight at 37°C. Cells were then sub-cultured (1% v/v) into 50ml BHI broth and incubated at 37°C for 24h under constant agitation (150 rpm). The bacterial suspensions were then inoculated (1% v/v) in 200ml BHI broth and grown in the same conditions to stationary phase (OD600nm of 0.9)."	"growth_protocol_ch2.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch2.1"
"Control bacteria at 37°C (common reference).  Total RNA isolated from 5 indepedent cultures (pooled after cDNA labeling)."	"source_name_ch1.1"
"Bacteria at 71°C"	"source_name_ch2.1"
"After reaching an OD600nm of 0.9, cell cultures were placed immediately in a shaking water bath along with another BHI flask carrying a type T thermocouple connected to a MultiPaq 21 datalogger (Datapaq Inc.) for temperature profile and the process lethality values monitoring in real time. Bacteria suspension were heated at 58°C to process lethality values of 2 and 3, at 60°C to a process lethality value of 3, or until a temperature of 71°C was reached. Just after heating, cell suspension was cooled in an iced water bath under constant agitation (150 rpm) until the temperature dropped back to no less than 37°C in order to avoid cold stress. Cell suspensions were then centrifuged and the remaining cell pellets were treated with RNA protect bacteria reagent (Qiagen Inc.) prior to freezing at -80°C."	"treatment_protocol_ch1.1"
"After reaching an OD600nm of 0.9, cell cultures were placed immediately in a shaking water bath along with another BHI flask carrying a type T thermocouple connected to a MultiPaq 21 datalogger (Datapaq Inc.) for temperature profile and the process lethality values monitoring in real time. Bacteria suspension were heated at 58°C to process lethality values of 2 and 3, at 60°C to a process lethality value of 3, or until a temperature of 71°C was reached. Just after heating, cell suspension was cooled in an iced water bath under constant agitation (150 rpm) until the temperature dropped back to no less than 37°C in order to avoid cold stress. Cell suspensions were then centrifuged and the remaining cell pellets were treated with RNA protect bacteria reagent (Qiagen Inc.) prior to freezing at -80°C."	"treatment_protocol_ch2.1"