Affymetrix Experiment Description: Ciprofloxacin Treatment

Experiment design

Experiment Type Treatment: antibotic treatment
Experiment Factors Standard growth condition + 20ng/ml ciprofloxacin
Reference Standard growth condition
Hybridization Strategy 1 single experiment

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 Add 100x ciprofloxacin to final concentration 20ng/ml when OD600 reached 0.2
Sampling 2 sample: 10min and 30min after adding ciprofloxacin
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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