all cell lines were grwn in RPMI media supplemented with 10% FCS and 1% P/S
Extracted molecule
genomic DNA
Extraction protocol
Genomic DNA was extracted from cell lines using the PureGene kit.
Label
biotin
Label protocol
as per manufacturer
Hybridization protocol
Genomic DNA was hybridized to high-density oligonucleotide arrays (Affymetrix, Santa Clara, CA) interrogating 238,000 SNP loci on all chromosomes except Y, with a median intermarker distance of 5.2 kb (mean 12.2 kb; www.affymetrix.com). Array experiments were performed according to manufacturers instructions.
Scan protocol
arrays were washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Description
Hybridized to 250K_Sty
Data processing
SNPs were genotyped by the Affymetrix Genotyping Tools Version 2.0 software. Affymetrix CEL-files where preprocessed by the following procedure: Raw intensities were read out and preprocessed with GenePattern (http://www.broadinstitute.org/cancer/software/genepattern/; snpFileCreator); here, default configuration was used. As next step, intensities of each sample is divided by the mean of the normals and multiplied by 2 to take into account that normals are assumed to be diploid on average.
