7 protocols
AccessionNameType
P-MTAB-30599
bioassay_data_transformation
All samples were normalised using a global median normalization to obtain log2-ratios as described in Buffart et al. Genes Chromosomes & Cancer: 47(11);994-1004 (2008).
P-MTAB-30598
bioassay_data_transformation
A wave smoothing correction was performed on the normalised data as described in: 'Smoothing waves in array CGH tumor profiles'; Van de Wiel et al. Bioinformatics:25(9);1099-1104 (2009).
P-MTAB-30600
image_acquisition
Following hybridization, the arrays were scanned using the MS 200 Microarray Scanner (Roche NimbleGen), according to the manufacturer’s instructions (NimbleGen Arrays User’s Guide – CGH and CNV Arrays, version 8.1).. (Parameters: Scanning hardware = OTHER: MS200 Microarray Scanner (Roche), Scanning software = Scanning software)
P-MTAB-30597
hybridization
The samples were purified using the MinElute PCR Purification Kit (Qiagen). Hybridization was performed using the manufacturer’s instructions (NimbleGen Arrays User’s Guide – CGH and CNV Arrays, version 8.1). (Parameters: Chamber type = OTHER: NimbleGen Hybridization System, Quantity of label target used = 1, Mass unit = Micro gram, Tiny time unit = seconds, Volume unit = Nano litre, temperature = 42)
P-MTAB-30601
labeling
Labeling was performed using the CGH Labeling Kit for Oligo Arrays (Enzo Life Sciences, Farmingdale, NY, USA) as follows: 1 ug DNA from the tumor and a human male or female reference (Kreatach Diagnostics, Amsterdam, The Netherlands) was denatured together with 20 ul random primers in reaction buffer for 10 min at 98 degrees C and placed on ice (4 degrees C) for 5 min. Next, primer extension was performed using 10 ul nucleotide mixes containing either Cyanine 3-dUTP or Cyanine 5-dUTP nucleotide mixes and 1 ul Klenow Exo-DNA polymerase were added while the samples were still at 4 degrees C. The tumor samples were labeled with Cyanine 3-dUTP and the human reference samples with Cyanine 5-dUTP. After mixing, the samples were incubated for 4 hours at 37 degrees C. The labeling reaction was terminated by adding the Stop Buffer to the mixture and cooling down to 4 degrees C. See also Buffart et al. Genes Chromosomes & Cancer: 47(11);994-1004 (2008). (Parameters: Amount of nucleic acid labeled = 1, Amplification = none, Mass unit = Micro gram)
P-MTAB-30602
nucleic_acid_extraction
DNA was isolated using the QIAamp DNA MiniKit (Qiagen, Hilden, Germany), according to the manufacturer's instructions. (Parameters: Extracted product = genomic_DNA, Amplification = none) Male and female reference genomic DNA samples were also prepared according to manufacturer's instructions.
P-MTAB-30613
 
All samples were from resected tumors that were fresh frozen. From these frozen tumors, sections were cut. All sections contained >70% tumor cells, as verified by a pathologist. Genomic DNA was later isolated using thse sections.