Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray
Date
2005-09-15
Authors
von Schaulburg, Kristian R
Rise, Matthew L
Cooper, Glenn A
Brown, Gordon D
Gibbs, A Ross
Nelson, Colleen C
Davidson, William S
Koop, Ben F
Journal Title
Journal ISSN
Volume Title
Publisher
BioMed Central
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.
Description
BioMed Central
Keywords
Centre for Biomedical Research
Citation
von Schaulburg, K et al. Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray. BMC Genomics 2005, 6 :126