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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 |
| Parameters |
Scaling: Scale to 1000 using all probe sets. |
| 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] |