Hybridized chips were washed and stained following the company's EukGE-WS2v5 protocol.
The gene chips were washed and scanned using standard Affymetrix protocols.
Chips were washed and stained with streptavidin R-phycoerythrin (Molecular Probes).
DNA chips were washed in the 2×SSC, 0.1% SDS solution for 20 min, with occasional gentle shaking.
After overnight incubation the hybridization solutions were recovered and chips were washed and prepared for scanning per the manufacturer's protocols.
Chips were washed, stained, scanned and the quality of the created dat-file images was evaluated by using Gene Operating Software GCOS 1.2 and MAS 5.0 Software (Affymetrix).
After hybridization, gene chips were washed on a Fluidics station (Affymetrix, Santa Clara, CA), stained, and then scanned using an Affymetrix Genearray scanner GSC3000, with 7G upgrade (Affymetrix).
Labeled DNA was hybridized to Affymetrix P. aeruginosa Genome Arrays, and chips were washed, stained and scanned as previously described [18].
The chips were washed three times with the binding buffer, then once with the binding buffer without Triton for 5 min, then once with 2 mM HEPES at pH 7.5.
After hybridization, chips were washed and stained with streptavidin-conjugated phycoerythrin dye (Invitrogen) enhanced with biotinylated goat anti-streptavidin antibody (Vector Laboratories, Burlingame, CA) utilizing an Affymetrix GeneChip® Fluidics Station 450 and GeneChip® Operating Software.
The hybridized chips were washed at 42°C for 5 min with 2× SSC containing 0.2% SDS and then washed with 0.2× SSC at room temperature for 5 min, before being dried at room temperature for scanning.
