Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]

Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress

rawData

scan

processedDataMatrix

An integrated genomic and proteomic analysis was undertaken to determine the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions relevant to low temperature and water activity conditions experienced during meat carcase chilling in cold air. The response of E. coli during exponential growth at 25°C aw 0.985, 14°C aw 0.985, 25°C aw 0.967 and, 14°C aw 0.967 was compared to that of a reference culture (35°C aw 0.993).

GROWTH_CONDITION

INDIVIDUAL

An integrated genomic and proteomic analysis was undertaken to determine the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions relevant to low temperature and water activity conditions experienced during meat carcase chilling in cold air. The response of E. coli during exponential growth at 25°C aw 0.985, 14°C aw 0.985, 25°C aw 0.967 and, 14°C aw 0.967 was compared to that of a reference culture (35°C aw 0.993).


Affymetrix:Protocol:Hybridization-Unknown

P-AFFY-6

Title: Affymetrix CEL analysis. Description:

P-G12006-2

According to Affymetrix E.coli Genome 2.0 array instructions. Genechip DNA labeling reagent.

P-MTAB-20302

Overnight cultures (20 h) were grown at 37C in a shaking waterbath in 250-ml Erlenmeyer flasks containing 25 ml of brain heart infusion broth (BHI) broth (Oxoid, Basingstoke, UK).

P-MTAB-20303

A 250 ul aliquot of the overnight (20 h) culture was dispensed into 25 ml of fresh BHI (aw 0.993) and grown at 35C in a shaking water bath. When this culture reached an OD600 of 0.1 ± 0.01, a 25 ul aliquot was dispensed into 25 ml of fresh BHI (aw 0.993) and grown at 35C in a shaking water bath. The culture was harvested upon reaching an OD600 of 0.1 ± 0.01.

P-MTAB-20304

A 250 ul aliquot of the overnight (20 h) culture was dispensed into 25 ml of fresh BHI (aw 0.985) and grown at 25C in a shaking water bath. When this culture reached an OD600 of 0.1 ± 0.01, a 25 ul aliquot was dispensed into 25 ml of fresh BHI (aw 0.985) and grown at 25C in a shaking water bath. The culture was harvested upon reaching an OD600 of 0.1 ± 0.01.

P-MTAB-20305

A 250 ul aliquot of the overnight (20 h) culture was dispensed into 25 ml of fresh BHI (aw 0.985) and grown at 14C in a shaking water bath. When this culture reached an OD600 of 0.1 ± 0.01, a 25 ul aliquot was dispensed into 25 ml of fresh BHI (aw 0.985) and grown at 14C in a shaking water bath. The culture was harvested upon reaching an OD600 of 0.1 ± 0.01.

P-MTAB-20306

A 250 ul aliquot of the overnight (20 h) culture was dispensed into 25 ml of fresh BHI (aw 0.967) and grown at 14C in a shaking water bath. When this culture reached an OD600 of 0.1 ± 0.01, a 25 ul aliquot was dispensed into 25 ml of fresh BHI (aw 0.967) and grown at 14C in a shaking water bath. The culture was harvested upon reaching an OD600 of 0.1 ± 0.01.

P-MTAB-20307

A 250 ul aliquot of the overnight (20 h) culture was dispensed into 25 ml of fresh BHI (aw 0.967) and grown at 25C in a shaking water bath. When this culture reached an OD600 of 0.1 ± 0.01, a 25 ul aliquot was dispensed into 25 ml of fresh BHI (aw 0.967) and grown at 25C in a shaking water bath. The culture was harvested upon reaching an OD600 of 0.1 ± 0.01.

P-MTAB-20308

The 25 ml culture was added to 5 ml of ice-cold phenol-ethanol (5:95) to stabilise the RNA and prevent degradation. The culture was immediately transferred to ice prior to RNA extraction. RNA samples were prepared using a Promega SV total RNA purification kit according to the manufacturer's instructions. RNA concentration was determined using a NanoPhotometer (Implen Pty). RNA quality was determined by 16S and 23S rRNA peak examination by the Bioanalyzer 2100 (Agilent, Santa Clara, CA) using an RNA nano chip. RNA was stored at -80C.

P-MTAB-20309

Gene expression analysis was carried out using GeneSpring GX 10.0 software (Agilent Technologies, Palo Alto, CA). Array data was normalized using the Robust Multi-Array Analysis (RMA) algorithm and samples below the 20th percentile of normalized intensity values were removed. Gene expression analysis was carried out using GeneSpring GX 10.0 software (Agilent Technologies, Palo Alto, CA). Significance analysis was conducted using one way analysis of variance (ANOVA) using the multiple correction testing method of Benjamini-Hochberg with a p-value cut-off of <0.01.

Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress

Submitter Supplied Information

Samples