The uracil glycosilase treatment, streptavidin/phycoerythrin labeling, hybridization and microarray scanning were performed as per Affymetrix chromatin immunoprecipitation assay protocol at The Centre for Applied Genomics (The Hospital for Sick Children, Toronto, ON, Canada).
RNA quality check, target labeling, GeneChip hybridization, and oligonucleotide microarray scanning were carried out at Seqwright (Houston, TX, USA) on the GeneChip Drosophila 2.0 Array (Affymetrix, Santa Clara, CA) following a standard Affymetrix protocol.
Biofilm modelling, confocal imaging, planktonic phase culturing, RNA isolation, cDNA labelling and microarray scanning were performed as previously described [ 5].
cDNA synthesis, labeling, hybridization, and microarray scanning were performed by the Centre for Genomics and Bioinformatics, Bloomington, Indiana.
cDNA synthesis, labeling, hybridization, and microarray scanning were performed by the Centre for Genomics and Bioinformatics, Bloomington, IN.
Target hybridization, washing, staining, and microarray scanning were conducted according to the standard GeneChip® Expression Analysis Technical Manual [ 83].
Microarray scanning was done by using a GenePix Personal 4100A scanner (Axon Instruments/Molecular Devices Corp., California, USA).
Images of microarray scans were quantified using GenePix.
Microarray scans were quantified using The Institute for Genomic Research TIGRR) SpotFinder module of TM4 http://www.tm4.org.
All microarray scans were inspected visually and checked for quality on the basis of the performance of negative, housekeeping and externally added Cy3/Cy5-prelabeled spiking controls.
Raw mean intensity data for each probe set pair of all the microarray scans were statistically analyzed by planned linear contrast [ 27] using SAS SAS Institutee, Cary, NC).
