Genomic DNA microarray for comparative genomic hybridization

Antoine M. Snijders, Richard L. Segraves, Stephanie Blackwood, Daniel Pinkel, Donna G. Albertson

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

This chapter describes a polymerase chain reaction (PCR)-based method for producing large quantities of BAC DNA, which aims at maximizing the representation of each bacterial artificial chromosome (BAC). Ligation-mediated PCR is used as a template in a Re-PCR reaction to generate DNA for spotting. Hybridization of fluorescently labeled genomic DNA for array CGH analysis involves distributing 1 g of dextran sulfate over the entire length of a 15-ml tube. While holding the tube horizontally, one needs to squirt in 5 ml of formamide. One needs to carefully aspirate and discard the supernatant, while wiping excess liquid from the tube with a tissue paper. One should be careful not to disturb the pellet. The next step involves placing the slides in the Stratalinker with arrays facing up. The arrays should be given a fixed amount of energy instead of the other available options the Stratalinker might have, such as autocrosslink or time. Overcross-linking the slide might result in a decrease in fluorescent hybridization signal.

Original languageEnglish (US)
Title of host publicationCell Biology, Four-Volume Set
PublisherElsevier Inc.
Pages445-454
Number of pages10
Volume3
ISBN (Print)9780121647308
DOIs
StatePublished - 2006

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

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    Snijders, A. M., Segraves, R. L., Blackwood, S., Pinkel, D., & Albertson, D. G. (2006). Genomic DNA microarray for comparative genomic hybridization. In Cell Biology, Four-Volume Set (Vol. 3, pp. 445-454). Elsevier Inc.. https://doi.org/10.1016/B978-012164730-8/50174-X