Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray
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...
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ftdoajarticles:oai:doaj.org/article:9d9540b236b64a78b7497cf03460ce46 2023-05-15T15:31:40+02:00 Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray Nelson Colleen C Gibbs A Ross Brown Gordon D Cooper Glenn A Rise Matthew L von Schalburg Kristian R Davidson William S Koop Ben F 2005-09-01T00:00:00Z https://doi.org/10.1186/1471-2164-6-126 https://doaj.org/article/9d9540b236b64a78b7497cf03460ce46 EN eng BMC http://www.biomedcentral.com/1471-2164/6/126 https://doaj.org/toc/1471-2164 doi:10.1186/1471-2164-6-126 1471-2164 https://doaj.org/article/9d9540b236b64a78b7497cf03460ce46 BMC Genomics, Vol 6, Iss 1, p 126 (2005) Biotechnology TP248.13-248.65 Genetics QH426-470 article 2005 ftdoajarticles https://doi.org/10.1186/1471-2164-6-126 2022-12-31T08:15:54Z 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. Article in Journal/Newspaper Atlantic salmon Directory of Open Access Journals: DOAJ Articles BMC Genomics 6 1 |
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Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
language |
English |
topic |
Biotechnology TP248.13-248.65 Genetics QH426-470 |
spellingShingle |
Biotechnology TP248.13-248.65 Genetics QH426-470 Nelson Colleen C Gibbs A Ross Brown Gordon D Cooper Glenn A Rise Matthew L von Schalburg Kristian R Davidson William S Koop Ben F Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray |
topic_facet |
Biotechnology TP248.13-248.65 Genetics QH426-470 |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Nelson Colleen C Gibbs A Ross Brown Gordon D Cooper Glenn A Rise Matthew L von Schalburg Kristian R Davidson William S Koop Ben F |
author_facet |
Nelson Colleen C Gibbs A Ross Brown Gordon D Cooper Glenn A Rise Matthew L von Schalburg Kristian R Davidson William S Koop Ben F |
author_sort |
Nelson Colleen C |
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 |
BMC |
publishDate |
2005 |
url |
https://doi.org/10.1186/1471-2164-6-126 https://doaj.org/article/9d9540b236b64a78b7497cf03460ce46 |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
BMC Genomics, Vol 6, Iss 1, p 126 (2005) |
op_relation |
http://www.biomedcentral.com/1471-2164/6/126 https://doaj.org/toc/1471-2164 doi:10.1186/1471-2164-6-126 1471-2164 https://doaj.org/article/9d9540b236b64a78b7497cf03460ce46 |
op_doi |
https://doi.org/10.1186/1471-2164-6-126 |
container_title |
BMC Genomics |
container_volume |
6 |
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1 |
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1766362198752362496 |