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Proceedings Paper

Comparative examination of probe labeling methods for microarray hybridization
Author(s): David I. Burke; Karen Woodward; Robert A. Setterquist; Ernest S. Kawasaki
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Paper Abstract

For detection of differential gene expression, confocal laser based scanners are now capable of analyzing microarrays using one to five wavelengths. This allows investigators to choose among several labeling methods. Here we compare direct incorporation and indirect methods (amino-allyl and dendrimers) for labeling cDNA probes. We assessed reproducible sensitivity of each probe preparation method in two ways. First, by comparing hybridization intensities for limit of signal detection and second by measuring the lowest detectable concentration of a known ratio of mixed DNA (spikes). Limit of detection assay was done using arrays of mixed targets consisting of a serially diluted human specific gene fragment (HU1) and an undiluted DNA of chloramphenicol acetyl tranferase (CAT) gene. Then, individual single target arrays of CAT and HU1 DNA were used to determine the lowest detectable spike ratio of each labeling method. The results of this study will be presented and their significance for the analysis of microarrays will be discussed.

Paper Details

Date Published: 4 June 2001
PDF: 8 pages
Proc. SPIE 4266, Microarrays: Optical Technologies and Informatics, (4 June 2001); doi: 10.1117/12.427979
Show Author Affiliations
David I. Burke, Packard BioChip Technologies, LLC (United States)
Karen Woodward, Packard BioChip Ventures (United States)
Robert A. Setterquist, Ambion, Inc. (United States)
Ernest S. Kawasaki, Packard BioChip Technologies, LLC (United States)


Published in SPIE Proceedings Vol. 4266:
Microarrays: Optical Technologies and Informatics
Michael L. Bittner; Yidong Chen; Andreas N. Dorsel; Edward R. Dougherty, Editor(s)

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