Methodology article

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

Kristian R von Schalburg¹ , Matthew L Rise² , Glenn A Cooper¹ , Gordon D Brown¹ , A Ross Gibbs¹ , Colleen C Nelson³ , William S Davidson⁴ and Ben F Koop¹

¹  Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5, Canada

²  Great Lakes WATER Institute, University of Wisconsin-Milwaukee, Milwaukee, WI, 53204, USA

³  The Prostate Centre at Vancouver General Hospital, Gene Array Facility, Vancouver, British Columbia, V6H 3Z6, Canada

⁴  Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada

author email corresponding author email

BMC Genomics 2005, 6:126doi:10.1186/1471-2164-6-126

Published:	15 September 2005

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.