|Avoid touching the surface of
the glass with your finersǯ Skin oils and other substances, such as
lotions or ink, can fluoresceǯ If the surface of the glass is noticeably dirty, it can be carefully cleaned with a nonabrasive laboratory tissue.
Array-CGH and bioinformatic analysis
Array-CGH was carried out using a 60-mer oligonucleotide-based microarray platform that allows molecular profiling of genomic aberrations with an overall median probe spatial resolution of 13 Kb (180K) (Agilent Technologies Array-CGH Kits). Human genomic DNA was used as reference DNA. Aliquots of 2 µg of DNA from samples were double-digested with RsaI and AluI for 2 hours at 37°C. After heat inactivation of the enzymes at 65°C for 20 minutes, each digested sample was labelled by random priming (Agilent Technologies) for 2 hours using Cy5-dUTP for patient/parent DNAs and Cy3-dUTP for reference DNAs. Labelled products were column purified with Illustra CyScribe GFX purification kit (GE Healthcare). After probe denaturation and pre-annealing with 5-25 µg of Cot-1 DNA, hybridization was performed at 65°C with rotation for 24 hours. After washing steps, following the manufacturer's instructions, the array was analyzed using an Agilent scanner and Feature Extraction software v.10.5. A graphical overview of the results was obtained using DNA Analytics software v.4.0. The chromosome aberration regions were calculated by ADM2 algorithm with a moving average window of 50 Kb. The microarray data are available in the ArrayExpress database () under accession number E-MEXP-3948. Full paper
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