Evaluation of potential reference genes in real-time RT-PCR studies of Atlantic salmon
Identifieur interne : 000262 ( Pmc/Curation ); précédent : 000261; suivant : 000263Evaluation of potential reference genes in real-time RT-PCR studies of Atlantic salmon
Auteurs : P L A. Olsvik [Norvège] ; Kai K. Lie [Norvège] ; Ann-Elise O. Jordal [Norvège] ; Tom O. Nilsen [Norvège] ; Ivar Hordvik [Norvège]Source :
- BMC Molecular Biology [ 1471-2199 ] ; 2005.
Abstract
Salmonid fishes are among the most widely studied model fish species but reports on systematic evaluation of reference genes in qRT-PCR studies is lacking.
The stability of six potential reference genes was examined in eight tissues of Atlantic salmon (
Overall, this work suggests that the EF1AA and EF1AB genes can be useful as reference genes in qRT-PCR examination of gene expression in the Atlantic salmon.
Url:
DOI: 10.1186/1471-2199-6-21
PubMed: 16293192
PubMed Central: 1314898
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Salmonid fishes are among the most widely studied model fish species but reports on systematic evaluation of reference genes in qRT-PCR studies is lacking.</p>
</sec>
<sec><title>Results</title>
<p>The stability of six potential reference genes was examined in eight tissues of Atlantic salmon (<italic>Salmo salar</italic>
), to determine the most suitable genes to be used in quantitative real-time RT-PCR analyses. The relative transcription levels of genes encoding 18S rRNA, S20 ribosomal protein, β-actin, glyceraldehyde-3P-dehydrogenase (GAPDH), and two paralog genes encoding elongation factor 1A (EF1A<sub>A </sub>
and EF1A<sub>B</sub>
) were quantified in gills, liver, head kidney, spleen, thymus, brain, muscle, and posterior intestine in six untreated adult fish, in addition to a group of individuals that went through smoltification. Based on calculations performed with the <italic>geNorm </italic>
VBA applet, which determines the most stable genes from a set of tested genes in a given cDNA sample, the ranking of the examined genes in adult Atlantic salmon was EF1A<sub>B</sub>
>EF1A<sub>A</sub>
>β-actin>18S rRNA>S20>GAPDH. When the same calculations were done on a total of 24 individuals from four stages in the smoltification process (presmolt, smolt, smoltified seawater and desmoltified freshwater), the gene ranking was EF1A<sub>B</sub>
>EF1A<sub>A</sub>
>S20>β-actin>18S rRNA>GAPDH.</p>
</sec>
<sec><title>Conclusion</title>
<p>Overall, this work suggests that the EF1A<sub>A </sub>
and EF1A<sub>B </sub>
genes can be useful as reference genes in qRT-PCR examination of gene expression in the Atlantic salmon.</p>
</sec>
</div>
</front>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Mol Biol</journal-id>
<journal-title>BMC Molecular Biology</journal-title>
<issn pub-type="epub">1471-2199</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
<publisher-loc>London</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">16293192</article-id>
<article-id pub-id-type="pmc">1314898</article-id>
<article-id pub-id-type="publisher-id">1471-2199-6-21</article-id>
<article-id pub-id-type="doi">10.1186/1471-2199-6-21</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Evaluation of potential reference genes in real-time RT-PCR studies of Atlantic salmon</article-title>
</title-group>
<contrib-group><contrib id="A1" corresp="yes" contrib-type="author"><name><surname>Olsvik</surname>
<given-names>Pål A</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>pal.olsvik@nifes.no</email>
</contrib>
<contrib id="A2" contrib-type="author"><name><surname>Lie</surname>
<given-names>Kai K</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>kai.lie@nifes.no</email>
</contrib>
<contrib id="A3" contrib-type="author"><name><surname>Jordal</surname>
<given-names>Ann-Elise O</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>ann-elise.jordal@nifes.no</email>
</contrib>
<contrib id="A4" contrib-type="author"><name><surname>Nilsen</surname>
<given-names>Tom O</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>Tom.Nilsen@bio.uib.no</email>
</contrib>
<contrib id="A5" contrib-type="author"><name><surname>Hordvik</surname>
<given-names>Ivar</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>ivar.hordvik@ifm.uib.no</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
National Institute of Nutrition and Seafood Research, Nordnesboder 2, N-5005 Bergen, Norway</aff>
<aff id="I2"><label>2</label>
Department of Biology, University of Bergen, Thormøhlensgate 55, N-5020 Bergen, Norway</aff>
<pub-date pub-type="collection"><year>2005</year>
</pub-date>
<pub-date pub-type="epub"><day>17</day>
<month>11</month>
<year>2005</year>
</pub-date>
<volume>6</volume>
<fpage>21</fpage>
<lpage>21</lpage>
<ext-link ext-link-type="uri" xlink:href="http://www.biomedcentral.com/1471-2199/6/21"></ext-link>
<history><date date-type="received"><day>22</day>
<month>7</month>
<year>2005</year>
</date>
<date date-type="accepted"><day>17</day>
<month>11</month>
<year>2005</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2005 Olsvik et al; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2005</copyright-year>
<copyright-holder>Olsvik et al; licensee BioMed Central Ltd.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0"></ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p>
<pmc-comment>
Olsvik
A
Pål
pal.olsvik@nifes.no
Evaluation of potential reference genes in real-time RT-PCR studies of Atlantic salmon
2005 BMC Molecular Biology 6(1): 21-. (2005) 1471-2199(2005)6:1<21> urn:ISSN:1471-2199 </pmc-comment>
</license>
</permissions>
<abstract><sec><title>Background</title>
<p>Salmonid fishes are among the most widely studied model fish species but reports on systematic evaluation of reference genes in qRT-PCR studies is lacking.</p>
</sec>
<sec><title>Results</title>
<p>The stability of six potential reference genes was examined in eight tissues of Atlantic salmon (<italic>Salmo salar</italic>
), to determine the most suitable genes to be used in quantitative real-time RT-PCR analyses. The relative transcription levels of genes encoding 18S rRNA, S20 ribosomal protein, β-actin, glyceraldehyde-3P-dehydrogenase (GAPDH), and two paralog genes encoding elongation factor 1A (EF1A<sub>A </sub>
and EF1A<sub>B</sub>
) were quantified in gills, liver, head kidney, spleen, thymus, brain, muscle, and posterior intestine in six untreated adult fish, in addition to a group of individuals that went through smoltification. Based on calculations performed with the <italic>geNorm </italic>
VBA applet, which determines the most stable genes from a set of tested genes in a given cDNA sample, the ranking of the examined genes in adult Atlantic salmon was EF1A<sub>B</sub>
>EF1A<sub>A</sub>
>β-actin>18S rRNA>S20>GAPDH. When the same calculations were done on a total of 24 individuals from four stages in the smoltification process (presmolt, smolt, smoltified seawater and desmoltified freshwater), the gene ranking was EF1A<sub>B</sub>
>EF1A<sub>A</sub>
>S20>β-actin>18S rRNA>GAPDH.</p>
</sec>
<sec><title>Conclusion</title>
<p>Overall, this work suggests that the EF1A<sub>A </sub>
and EF1A<sub>B </sub>
genes can be useful as reference genes in qRT-PCR examination of gene expression in the Atlantic salmon.</p>
</sec>
</abstract>
</article-meta>
</front>
</pmc>
</record>
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