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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
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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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