SurePrint glass slide microarrays (Agilent Technologies Inc.) were manufactured with 60-nt DNA oligomers synthesized in 60,000 features on eight replicate arrays per slide. PathoChip v2a and v2b contained 60,000 probes to unique target regions and conserved plus saturation target regions, respectively. PathoChip v3 contained 37,704 probes to unique targets and 23,627 probes to conserved targets or to saturate known oncogenic and pathogenic viral agents.
Labeled samples were hybridized to microarrays as described in the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol (version 7.2, G4410-90010). Master mixes containing aCGH blocking agent, HI-RPM hybridization buffer, and Cot-1 DNA (pilot assays only) were added to a mixture of the entire labeled test sample and the xhh DNA control sample, denatured, and hybridized to arrays under 8-chamber gasket slides at 65°C with 20-rpm rotation for 40 h in an Agilent hybridization oven. Arrays were processed using wash procedure A and scanned on an Agilent SureScan G4900DA microarray scanner.
Labeled samples were hybridized to microarrays as described in the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol (version 7.2, G4410-90010). Master mixes containing aCGH blocking agent, HI-RPM hybridization buffer, and Cot-1 DNA (pilot assays only) were added to a mixture of the entire labeled test sample and the xhh DNA control sample, denatured, and hybridized to arrays under 8-chamber gasket slides at 65°C with 20-rpm rotation for 40 h in an Agilent hybridization oven. Arrays were processed using wash procedure A and scanned on an Agilent SureScan G4900DA microarray scanner.