Affymetrix Experiment Description: Standard Control

Experiment design

Experiment Type Standard control
Experiment Factors Standard growth condition
Reference None
Hybridization Strategy 5 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 None
Sampling OD600 equals to 0.2 (mid log phase)
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

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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