All cell lines were grown in DMEM or RPMI-1640 supplemented with 10% FBS
Extracted molecule
genomic DNA
Extraction protocol
Qiagen DNA extraction kit was used according to the manufacturer's instructions
Label
biotin
Label protocol
Affymetrix 100K protocol
Hybridization protocol
Affymetrix 100K protocol
Scan protocol
Affymetrix 100K protocol
Description
MDA435_hind
Data processing
Affymetrix 100K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization. Ninety normal samples were downloaded from the Affymetrix website (http://www.affymetrix.com/support/technical/byproduct.affx?product=100k) and analyzed at the same time. One CEL file for each set (Xba and Hind) with the median signal intensity across the set was selected as the reference array. The dChip-normalized signal intensities were converted to log2 ratios and segmented as follows. For each autosomal probe set, the log2 tumor/normal ratio of each tumor sample was calculated using the average intensity for each probe set in the normal set. The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment.
