SurePrint G3 Human CGH Microarray Kit, 4x180K

Protocol tips

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	Avoid touching the surface of the glass with your finersǯ 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.

Protocol tips
Avoid touching the surface of the glass with your finersǯ 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.

Publication protocol

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.

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Manufacturer protocol

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