Affymetrix Experiment Description: Acid Shock at pH 2

Experiment design

Experiment Type Treatment: environment change
Experiment Factors Standard growth condition + acid shock at pH 2
Reference Standard growth condition
Hybridization Strategy 2 replicates from independent culture

Sample description

Strain E. coli K12 MG1655
StrainID in ASAP MG1655
Medium MOPS minimal medium + 0.1% Glucose, pH 7.2
Growth Condition 100ml culture in a 1L flask, 37C, 220rpm waterbath
Sample manipulation Adjusted the culture pH to 2 with HCl when OD600 reached 0.2.
Sampling 1 sample: Acid shock at pH 2 for 10 min
RNA stabilization Qiagen Bacteria RNA protect reagent
RNA extraction Epicentre Masterpure total RNA purification kit [protocol]

Labeling and hybridization

Labeling Protocol Modified from standard Affymetrix protocol [protocol]
Hybridization Protocol Standard protocol [Affymetrix]
Hybiridization parameters 45C, 60rpm, 16hour in an air incubator
Wash Fluidics Station 400, Standard protocol [Affymetrix]
Scanner HP Genechip Scanner
Scanning parameters Standard settings. Every chip was scanned twice.
Software Affymetrix Microarray Suite v5.0

Data extraction and post process

Software Affymetrix Microarray Suite v5.0
Algorithm Statistical algorithm
Parameters

Scaling: Scale to 1000 using all probe sets.
Normalization: No normalization.
Alpha1=0.04, Alpha2=0.06, Tau=0.015

Post Processing ETCN were calculated. More information.
Processed Data ASAP
Raw Data Upon Request. More information

Array Design

Name of Array E. coli antisense genome array (P/N: 510052)
URL to Affymetrix [Affymetrix]

 


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