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Fish and chips : various methodologies demonstrate utility of a 16,006-gene salmonid microarray

Von Schalburg, Kristian R., Rice, Matthew L., Cooper, Glenn A., Brown, Gordon D., Gibbs, A. Ross, Nelson, Colleen C., Davidson, William S., & Koop, Ben F. (2005) Fish and chips : various methodologies demonstrate utility of a 16,006-gene salmonid microarray. BMC Genomics, 6(126), pp. 1-8.

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Abstract

Background We have developed and fabricated a salmonid microarray containing cDNAs representing 16,006 genes. The genes spotted on the array have been stringently selected from Atlantic salmon and rainbow trout expressed sequence tag (EST) databases. The EST databases presently contain over 300,000 sequences from over 175 salmonid cDNA libraries derived from a wide variety of tissues and different developmental stages. In order to evaluate the utility of the microarray, a number of hybridization techniques and screening methods have been developed and tested.

Results We have analyzed and evaluated the utility of a microarray containing 16,006 (16K) salmonid cDNAs in a variety of potential experimental settings. We quantified the amount of transcriptome binding that occurred in cross-species, organ complexity and intraspecific variation hybridization studies. We also developed a methodology to rapidly identify and confirm the contents of a bacterial artificial chromosome (BAC) library containing Atlantic salmon genomic DNA.

Conclusion We validate and demonstrate the usefulness of the 16K microarray over a wide range of teleosts, even for transcriptome targets from species distantly related to salmonids. We show the potential of the use of the microarray in a variety of experimental settings through hybridization studies that examine the binding of targets derived from different organs and tissues. Intraspecific variation in transcriptome expression is evaluated and discussed. Finally, BAC hybridizations are demonstrated as a rapid and accurate means to identify gene content.

Impact and interest:

138 citations in Scopus
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138 citations in Web of Science®

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ID Code: 11989
Item Type: Journal Article
Additional Information: The contents of this journal can be freely accessed online via the journal’s web page (see hypertext link).
DOI: 10.1186/1471-2164-6-126
ISSN: 1471-2164
Subjects: Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000)
Divisions: Past > QUT Faculties & Divisions > Faculty of Science and Technology
Current > Institutes > Institute of Health and Biomedical Innovation
Past > Schools > School of Life Sciences
Copyright Owner: Copyright 2005 BioMed Central Ltd.
Copyright Statement: Reproduced in accordance with the copyright policy of the publisher.
Deposited On: 16 Jan 2008
Last Modified: 29 Feb 2012 23:29

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