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

dc.contributor.authorvon Schaulburg, Kristian R
dc.contributor.authorRise, Matthew L
dc.contributor.authorCooper, Glenn A
dc.contributor.authorBrown, Gordon D
dc.contributor.authorGibbs, A Ross
dc.contributor.authorNelson, Colleen C
dc.contributor.authorDavidson, William S
dc.contributor.authorKoop, Ben F
dc.date.accessioned2014-07-14T17:08:27Z
dc.date.available2014-07-14T17:08:27Z
dc.date.copyright2005en_US
dc.date.issued2005-09-15
dc.descriptionBioMed Centralen_US
dc.description.abstractBackground: 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.en_US
dc.description.reviewstatusRevieweden_US
dc.description.scholarlevelFacultyen_US
dc.identifier.citationvon Schaulburg, K et al. Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray. BMC Genomics 2005, 6 :126en_US
dc.identifier.urihttp://www.biomedcentral.com/1471-2164/6/126
dc.identifier.urihttp://dx.doi.org/10.1186/1471-2164-6-126
dc.identifier.urihttp://hdl.handle.net/1828/5450
dc.language.isoenen_US
dc.publisherBioMed Centralen_US
dc.titleFish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarrayen_US
dc.typeArticleen_US

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