Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray
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...
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ftqueensland:oai:eprints.qut.edu.au:11989 2024-02-04T09:58:56+01:00 Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray Von Schalburg, Kristian Rice, Matthew Cooper, Glenn Brown, Gordon Gibbs, A Nelson, Colleen Davidson, William Koop, Ben 2005 application/pdf https://eprints.qut.edu.au/11989/ unknown BioMed Central Ltd. https://eprints.qut.edu.au/11989/1/11989.pdf doi:10.1186/1471-2164-6-126 Von Schalburg, Kristian, Rice, Matthew, Cooper, Glenn, Brown, Gordon, Gibbs, A, Nelson, Colleen, Davidson, William, & Koop, Ben (2005) Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray. BMC Genomics, 6, pp. 126-133. https://eprints.qut.edu.au/11989/ Faculty of Science and Technology; Biogeoscience; Institute of Health and Biomedical Innovation free_to_read Consult author(s) regarding copyright matters This work is covered by copyright. Unless the document is being made available under a Creative Commons Licence, you must assume that re-use is limited to personal use and that permission from the copyright owner must be obtained for all other uses. If the document is available under a Creative Commons License (or other specified license) then refer to the Licence for details of permitted re-use. It is a condition of access that users recognise and abide by the legal requirements associated with these rights. If you believe that this work infringes copyright please provide details by email to qut.copyright@qut.edu.au BMC Genomics Contribution to Journal 2005 ftqueensland https://doi.org/10.1186/1471-2164-6-126 2024-01-08T23:21:52Z 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. Article in Journal/Newspaper Atlantic salmon Queensland University of Technology: QUT ePrints BMC Genomics 6 1 |
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Open Polar |
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Queensland University of Technology: QUT ePrints |
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ftqueensland |
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unknown |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Von Schalburg, Kristian Rice, Matthew Cooper, Glenn Brown, Gordon Gibbs, A Nelson, Colleen Davidson, William Koop, Ben |
spellingShingle |
Von Schalburg, Kristian Rice, Matthew Cooper, Glenn Brown, Gordon Gibbs, A Nelson, Colleen Davidson, William Koop, Ben Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray |
author_facet |
Von Schalburg, Kristian Rice, Matthew Cooper, Glenn Brown, Gordon Gibbs, A Nelson, Colleen Davidson, William Koop, Ben |
author_sort |
Von Schalburg, Kristian |
title |
Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray |
title_short |
Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray |
title_full |
Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray |
title_fullStr |
Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray |
title_full_unstemmed |
Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray |
title_sort |
fish and chips: various methodologies demonstrate utility of a 16,006-gene salmonid microarray |
publisher |
BioMed Central Ltd. |
publishDate |
2005 |
url |
https://eprints.qut.edu.au/11989/ |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
BMC Genomics |
op_relation |
https://eprints.qut.edu.au/11989/1/11989.pdf doi:10.1186/1471-2164-6-126 Von Schalburg, Kristian, Rice, Matthew, Cooper, Glenn, Brown, Gordon, Gibbs, A, Nelson, Colleen, Davidson, William, & Koop, Ben (2005) Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray. BMC Genomics, 6, pp. 126-133. https://eprints.qut.edu.au/11989/ Faculty of Science and Technology; Biogeoscience; Institute of Health and Biomedical Innovation |
op_rights |
free_to_read Consult author(s) regarding copyright matters This work is covered by copyright. Unless the document is being made available under a Creative Commons Licence, you must assume that re-use is limited to personal use and that permission from the copyright owner must be obtained for all other uses. If the document is available under a Creative Commons License (or other specified license) then refer to the Licence for details of permitted re-use. It is a condition of access that users recognise and abide by the legal requirements associated with these rights. If you believe that this work infringes copyright please provide details by email to qut.copyright@qut.edu.au |
op_doi |
https://doi.org/10.1186/1471-2164-6-126 |
container_title |
BMC Genomics |
container_volume |
6 |
container_issue |
1 |
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1789963522674786304 |