Fish and Chips: Various Methodologies Demonstrate Utility of a 16,006-Gene Salmonid Microarray

Background: We have developed and fabricated a salmonid microarray containing cDNAsrepresenting 16,006 genes. The genes spotted on the array have been stringently selected fromAtlantic salmon and rainbow trout expressed sequence tag (EST) databases. The EST databasespresently contain over 300,000 sequences from over 175 salmonid cDNA libraries derived from awide variety of tissues and different developmental stages. In order to evaluate the utility of themicroarray, a number of hybridization techniques and screening methods have been developed andtested.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 oftranscriptome binding that occurred in cross-species, organ complexity and intraspecific variationhybridization studies. We also developed a methodology to rapidly identify and confirm thecontents of a bacterial artificial chromosome (BAC) library containing Atlantic salmon genomicDNA.Conclusion: We validate and demonstrate the usefulness of the 16K microarray over a widerange of teleosts, even for transcriptome targets from species distantly related to salmonids. Weshow the potential of the use of the microarray in a variety of experimental settings throughhybridization studies that examine the binding of targets derived from different organs and tissues.Intraspecific variation in transcriptome expression is evaluated and discussed. Finally, BAChybridizations are demonstrated as a rapid and accurate means to identify gene content.