Development and experimental validation of a 20K Atlantic cod (Gadus morhua) oligonucleotide microarray based on a collection of over 150,000 ESTs
The collapse of Atlantic cod (Gadus morhua) wild populations strongly impacted the Atlantic cod fishery and led to the development of cod aquaculture. In order to improve aquaculture and broodstock quality, we need to gain knowledge of genes and pathways involved in Atlantic cod responses to pathoge...
Published in: | Marine Biotechnology |
---|---|
Main Authors: | , , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
2011
|
Subjects: | |
Online Access: | https://doi.org/10.1007/s10126-010-9335-6 https://nrc-publications.canada.ca/eng/view/accepted/?id=3f96cd1a-286b-402c-8b3a-e7abd2b8e180 https://nrc-publications.canada.ca/eng/view/object/?id=3f96cd1a-286b-402c-8b3a-e7abd2b8e180 https://nrc-publications.canada.ca/fra/voir/objet/?id=3f96cd1a-286b-402c-8b3a-e7abd2b8e180 |
id |
ftnrccanada:oai:cisti-icist.nrc-cnrc.ca:cistinparc:19770588 |
---|---|
record_format |
openpolar |
spelling |
ftnrccanada:oai:cisti-icist.nrc-cnrc.ca:cistinparc:19770588 2023-05-15T15:26:18+02:00 Development and experimental validation of a 20K Atlantic cod (Gadus morhua) oligonucleotide microarray based on a collection of over 150,000 ESTs Booman, Marije Borza, Tudor Feng, Charles Y. Hori, Tiago S. Higgins, Brent Culf, Adrian Léger, Daniel Chute, Ian C. Belkaid, Anissa Rise, Marlies Gamperl, A. Kurt Hubert, Sophie Kimball, Jennifer Ouellette, Rodney J. Johnson, Stewart C. Bowman, Sharen Rise, Matthew L. 2011-08-01 text https://doi.org/10.1007/s10126-010-9335-6 https://nrc-publications.canada.ca/eng/view/accepted/?id=3f96cd1a-286b-402c-8b3a-e7abd2b8e180 https://nrc-publications.canada.ca/eng/view/object/?id=3f96cd1a-286b-402c-8b3a-e7abd2b8e180 https://nrc-publications.canada.ca/fra/voir/objet/?id=3f96cd1a-286b-402c-8b3a-e7abd2b8e180 eng eng Marine Biotechnology, Volume: 13, Issue: 4, Publication date: 2011-08-01, Pages: 733–750 doi:10.1007/s10126-010-9335-6 Aquaculture Atlantic cod Gene expression profiling Microarray article 2011 ftnrccanada https://doi.org/10.1007/s10126-010-9335-6 2021-09-01T06:25:49Z The collapse of Atlantic cod (Gadus morhua) wild populations strongly impacted the Atlantic cod fishery and led to the development of cod aquaculture. In order to improve aquaculture and broodstock quality, we need to gain knowledge of genes and pathways involved in Atlantic cod responses to pathogens and other stressors. The Atlantic Cod Genomics and Broodstock Development Project has generated over 150,000 expressed sequence tags from 42 cDNA libraries representing various tissues, developmental stages, and stimuli. We used this resource to develop an Atlantic cod oligonucleotide microarray containing 20,000 unique probes. Selection of sequences from the full range of cDNA libraries enables application of the microarray for a broad spectrum of Atlantic cod functional genomics studies. We included sequences that were highly abundant in suppression subtractive hybridization (SSH) libraries, which were enriched for transcripts responsive to pathogens or other stressors. These sequences represent genes that potentially play an important role in stress and/or immune responses, making the microarray particularly useful for studies of Atlantic cod gene expression responses to immune stimuli and other stressors. To demonstrate its value, we used the microarray to analyze the Atlantic cod spleen response to stimulation with formalin-killed, atypical Aeromonas salmonicida, resulting in a gene expression profile that indicates a strong innate immune response. These results were further validated by quantitative PCR analysis and comparison to results from previous analysis of an SSH library. This study shows that the Atlantic cod 20K oligonucleotide microarray is a valuable new tool for Atlantic cod functional genomics research. © 2010 The Author(s). Peer reviewed: Yes NRC publication: Yes Article in Journal/Newspaper atlantic cod Gadus morhua National Research Council Canada: NRC Publications Archive Marine Biotechnology 13 4 733 750 |
institution |
Open Polar |
collection |
National Research Council Canada: NRC Publications Archive |
op_collection_id |
ftnrccanada |
language |
English |
topic |
Aquaculture Atlantic cod Gene expression profiling Microarray |
spellingShingle |
Aquaculture Atlantic cod Gene expression profiling Microarray Booman, Marije Borza, Tudor Feng, Charles Y. Hori, Tiago S. Higgins, Brent Culf, Adrian Léger, Daniel Chute, Ian C. Belkaid, Anissa Rise, Marlies Gamperl, A. Kurt Hubert, Sophie Kimball, Jennifer Ouellette, Rodney J. Johnson, Stewart C. Bowman, Sharen Rise, Matthew L. Development and experimental validation of a 20K Atlantic cod (Gadus morhua) oligonucleotide microarray based on a collection of over 150,000 ESTs |
topic_facet |
Aquaculture Atlantic cod Gene expression profiling Microarray |
description |
The collapse of Atlantic cod (Gadus morhua) wild populations strongly impacted the Atlantic cod fishery and led to the development of cod aquaculture. In order to improve aquaculture and broodstock quality, we need to gain knowledge of genes and pathways involved in Atlantic cod responses to pathogens and other stressors. The Atlantic Cod Genomics and Broodstock Development Project has generated over 150,000 expressed sequence tags from 42 cDNA libraries representing various tissues, developmental stages, and stimuli. We used this resource to develop an Atlantic cod oligonucleotide microarray containing 20,000 unique probes. Selection of sequences from the full range of cDNA libraries enables application of the microarray for a broad spectrum of Atlantic cod functional genomics studies. We included sequences that were highly abundant in suppression subtractive hybridization (SSH) libraries, which were enriched for transcripts responsive to pathogens or other stressors. These sequences represent genes that potentially play an important role in stress and/or immune responses, making the microarray particularly useful for studies of Atlantic cod gene expression responses to immune stimuli and other stressors. To demonstrate its value, we used the microarray to analyze the Atlantic cod spleen response to stimulation with formalin-killed, atypical Aeromonas salmonicida, resulting in a gene expression profile that indicates a strong innate immune response. These results were further validated by quantitative PCR analysis and comparison to results from previous analysis of an SSH library. This study shows that the Atlantic cod 20K oligonucleotide microarray is a valuable new tool for Atlantic cod functional genomics research. © 2010 The Author(s). Peer reviewed: Yes NRC publication: Yes |
format |
Article in Journal/Newspaper |
author |
Booman, Marije Borza, Tudor Feng, Charles Y. Hori, Tiago S. Higgins, Brent Culf, Adrian Léger, Daniel Chute, Ian C. Belkaid, Anissa Rise, Marlies Gamperl, A. Kurt Hubert, Sophie Kimball, Jennifer Ouellette, Rodney J. Johnson, Stewart C. Bowman, Sharen Rise, Matthew L. |
author_facet |
Booman, Marije Borza, Tudor Feng, Charles Y. Hori, Tiago S. Higgins, Brent Culf, Adrian Léger, Daniel Chute, Ian C. Belkaid, Anissa Rise, Marlies Gamperl, A. Kurt Hubert, Sophie Kimball, Jennifer Ouellette, Rodney J. Johnson, Stewart C. Bowman, Sharen Rise, Matthew L. |
author_sort |
Booman, Marije |
title |
Development and experimental validation of a 20K Atlantic cod (Gadus morhua) oligonucleotide microarray based on a collection of over 150,000 ESTs |
title_short |
Development and experimental validation of a 20K Atlantic cod (Gadus morhua) oligonucleotide microarray based on a collection of over 150,000 ESTs |
title_full |
Development and experimental validation of a 20K Atlantic cod (Gadus morhua) oligonucleotide microarray based on a collection of over 150,000 ESTs |
title_fullStr |
Development and experimental validation of a 20K Atlantic cod (Gadus morhua) oligonucleotide microarray based on a collection of over 150,000 ESTs |
title_full_unstemmed |
Development and experimental validation of a 20K Atlantic cod (Gadus morhua) oligonucleotide microarray based on a collection of over 150,000 ESTs |
title_sort |
development and experimental validation of a 20k atlantic cod (gadus morhua) oligonucleotide microarray based on a collection of over 150,000 ests |
publishDate |
2011 |
url |
https://doi.org/10.1007/s10126-010-9335-6 https://nrc-publications.canada.ca/eng/view/accepted/?id=3f96cd1a-286b-402c-8b3a-e7abd2b8e180 https://nrc-publications.canada.ca/eng/view/object/?id=3f96cd1a-286b-402c-8b3a-e7abd2b8e180 https://nrc-publications.canada.ca/fra/voir/objet/?id=3f96cd1a-286b-402c-8b3a-e7abd2b8e180 |
genre |
atlantic cod Gadus morhua |
genre_facet |
atlantic cod Gadus morhua |
op_relation |
Marine Biotechnology, Volume: 13, Issue: 4, Publication date: 2011-08-01, Pages: 733–750 doi:10.1007/s10126-010-9335-6 |
op_doi |
https://doi.org/10.1007/s10126-010-9335-6 |
container_title |
Marine Biotechnology |
container_volume |
13 |
container_issue |
4 |
container_start_page |
733 |
op_container_end_page |
750 |
_version_ |
1766356809873883136 |