Unrestricted HD-CGH Microarray ISCA v2, 4x44k

Protocol tips

Upstream tips	Protocol tips	Downstream 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.

Upstream 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

CGH assay and analysis.
Genomic DNA was isolated from the melanoma cell lines and PBMCs of a healthy female donor using the QIAamp DNA Mini Kit (QIAGEN), and 1.5 μg was fragmented, labeled, purified, and hybridized to Agilent 2 × 105 K arrays according to the Agilent Oligo Nucleotide Array–Based CGH for Genomic DNA Analysis (version 6.2.1) protocol. Data were extracted using Agilent’s Feature Extraction Software. Copy number variation was measured according to the Partek Genomic Suite. After circular binary segmentation normalization, copy number gains and losses were detected using a hidden Markov model algorithm in the Partek copy number workflow for unpaired samples. Amplifications were defined as segments with log2 ratios greater than 0.15. Deletions were defined as segments with log2 ratios less than –0.3. Segments were defined as regions that differed from neighboring regions by at least 10 markers. The regions identified were annotated using NCBI’s RefSeq hg19. Microarray data were deposited in the GEO database (GEO GSE44850).

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Manufacturer protocol

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