6 protocols
ID_REF = VALUE = normalized log10 ratio Cy5/Cy3
Scanned on a GenePix 4000B scanner or an Agilent high-resolution C scanner.
Signal intensities were evalutated using Feature Extraction software (log ratios from Feature Extraction files included in Sample tables) and Genomic Workbench was used to analyze array data and make breakpoint predictions (Genomic Workbench data and README file provided as supplementary files on the Series record).
Labeled DNA and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
Genomic DNA, 0.5-1ug, from patient samples and controls were Cy3/Cy5 labeled with Agilent Genomic DNA Enzymatic Labeling Kit following manufacture's protocol
Genomic DNA was extracted from peripheral blood or cell lines using Gentra Puregene DNA Extraction kit following manufacturers protocol