Functional genomics resources for the North Atlantic copepod, Calanus finmarchicus: EST database and physiological microarray
The copepod, Calanus finmarchicus is a keystone species for the North Atlantic. Because of recent changes in the geographic distribution of this species, there are questions as to how this organism responds physiologically to environmental cues. Molecular techniques allow for examination and new und...
Published in: | Comparative Biochemistry and Physiology Part D: Genomics and Proteomics |
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ftpubmed:oai:pubmedcentral.nih.gov:3586334 2023-05-15T15:47:55+02:00 Functional genomics resources for the North Atlantic copepod, Calanus finmarchicus: EST database and physiological microarray Lenz, Petra H. Unal, Ebru Hassett, R. Patrick Smith, Christine M. Bucklin, Ann Christie, Andrew E. Towle, David W. 2011-12-29 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3586334 http://www.ncbi.nlm.nih.gov/pubmed/22277925 https://doi.org/10.1016/j.cbd.2011.12.001 en eng http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3586334 http://www.ncbi.nlm.nih.gov/pubmed/22277925 http://dx.doi.org/10.1016/j.cbd.2011.12.001 Article Text 2011 ftpubmed https://doi.org/10.1016/j.cbd.2011.12.001 2013-09-04T20:33:23Z The copepod, Calanus finmarchicus is a keystone species for the North Atlantic. Because of recent changes in the geographic distribution of this species, there are questions as to how this organism responds physiologically to environmental cues. Molecular techniques allow for examination and new understanding of these physiological changes. Here, we describe the development of a microarray for high-throughput studies of the physiological ecology of C. finmarchicus. An EST database was generated for this species using a normalized cDNA library derived from adult and sub-adult individuals. Sequence data were clustered into contigs and annotated using Blastx. Target transcripts were selected, and unique, 50 base-pair, oligomer probes were generated for 995 genes. Blast2GO processing provided detailed information on gene function. The selected targets included broad representation of biological processes, cellular components, and molecular functions. The microarray was tested in two sets of comparisons: adult females maintained at different food concentrations and field-caught sub-adults showing differences in lipid storage. Up-regulated and down-regulated transcripts were identified for both comparisons. Only a small subset of the genes up-regulated in low food individuals were also up-regulated in lipid-poor animals; no overlap was seen between the genes down-regulated in the two comparisons. Text Calanus finmarchicus North Atlantic PubMed Central (PMC) Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 7 2 110 123 |
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Article Lenz, Petra H. Unal, Ebru Hassett, R. Patrick Smith, Christine M. Bucklin, Ann Christie, Andrew E. Towle, David W. Functional genomics resources for the North Atlantic copepod, Calanus finmarchicus: EST database and physiological microarray |
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The copepod, Calanus finmarchicus is a keystone species for the North Atlantic. Because of recent changes in the geographic distribution of this species, there are questions as to how this organism responds physiologically to environmental cues. Molecular techniques allow for examination and new understanding of these physiological changes. Here, we describe the development of a microarray for high-throughput studies of the physiological ecology of C. finmarchicus. An EST database was generated for this species using a normalized cDNA library derived from adult and sub-adult individuals. Sequence data were clustered into contigs and annotated using Blastx. Target transcripts were selected, and unique, 50 base-pair, oligomer probes were generated for 995 genes. Blast2GO processing provided detailed information on gene function. The selected targets included broad representation of biological processes, cellular components, and molecular functions. The microarray was tested in two sets of comparisons: adult females maintained at different food concentrations and field-caught sub-adults showing differences in lipid storage. Up-regulated and down-regulated transcripts were identified for both comparisons. Only a small subset of the genes up-regulated in low food individuals were also up-regulated in lipid-poor animals; no overlap was seen between the genes down-regulated in the two comparisons. |
format |
Text |
author |
Lenz, Petra H. Unal, Ebru Hassett, R. Patrick Smith, Christine M. Bucklin, Ann Christie, Andrew E. Towle, David W. |
author_facet |
Lenz, Petra H. Unal, Ebru Hassett, R. Patrick Smith, Christine M. Bucklin, Ann Christie, Andrew E. Towle, David W. |
author_sort |
Lenz, Petra H. |
title |
Functional genomics resources for the North Atlantic copepod, Calanus finmarchicus: EST database and physiological microarray |
title_short |
Functional genomics resources for the North Atlantic copepod, Calanus finmarchicus: EST database and physiological microarray |
title_full |
Functional genomics resources for the North Atlantic copepod, Calanus finmarchicus: EST database and physiological microarray |
title_fullStr |
Functional genomics resources for the North Atlantic copepod, Calanus finmarchicus: EST database and physiological microarray |
title_full_unstemmed |
Functional genomics resources for the North Atlantic copepod, Calanus finmarchicus: EST database and physiological microarray |
title_sort |
functional genomics resources for the north atlantic copepod, calanus finmarchicus: est database and physiological microarray |
publishDate |
2011 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3586334 http://www.ncbi.nlm.nih.gov/pubmed/22277925 https://doi.org/10.1016/j.cbd.2011.12.001 |
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Calanus finmarchicus North Atlantic |
genre_facet |
Calanus finmarchicus North Atlantic |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3586334 http://www.ncbi.nlm.nih.gov/pubmed/22277925 http://dx.doi.org/10.1016/j.cbd.2011.12.001 |
op_doi |
https://doi.org/10.1016/j.cbd.2011.12.001 |
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Comparative Biochemistry and Physiology Part D: Genomics and Proteomics |
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7 |
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2 |
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110 |
op_container_end_page |
123 |
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1766382892355682304 |