Reference genes identified in the silkworm Bombyx mori during metamorphism based on oligonucleotide microarray and confirmed by qRT‐PCR
Identifieur interne : 001607 ( Main/Exploration ); précédent : 001606; suivant : 001608Reference genes identified in the silkworm Bombyx mori during metamorphism based on oligonucleotide microarray and confirmed by qRT‐PCR
Auteurs : Gen-Hong Wang [République populaire de Chine] ; Qing-You Xia [République populaire de Chine] ; Dao-Jun Cheng [République populaire de Chine] ; Jun Duan [République populaire de Chine] ; Ping Zhao [République populaire de Chine] ; Jie Chen [République populaire de Chine] ; Li Zhu [République populaire de Chine]Source :
- Insect Science [ 1672-9609 ] ; 2008-10.
English descriptors
- Teeft :
- Actin, Authors journal compilation institute, Bombyx, Bombyx mori, Candidate reference genes, Chinese academy, Control genes, Cytoplasmic, Cytoplasmic actin, Data normalization, Developmental stage, Developmental stages, Expression levels, Expression pattern, Expression stability, Fifth instar, Further validation, Gene, Gene expression normalization, Gene expression quantification, Genome, Genorm, Genorm software, Housekeeping genes, Insect science, Instar, Internal controls, Microarray, Mori, Mrna, Normalization, Normalization factor, Normfinder, Oligonucleotide microarray, Optimal number, Primer, Program normfinder, Proteasome beta subunit, Protein synthesis, Reference gene, Reference gene candidates, Reference genes, Ribosomal, Ribosomal protein, Ribosomal protein genes, Silkworm, Silkworm bombyx mori, Stable genes, Stable reference genes, Subunit, Translation initiation factor, Translation initiation factors, Wang, Zhang, Zoology.
Abstract
Gene expression quantification at mRNA level is very important for post‐genomic studies, as gene expression level is the reflection of the special biological function of the target gene. Methods used for gene expression quantification, such as microarray or quantitative real‐time polymerase chain reaction (qRT‐PCR), require stable expressed reference genes. Thus, finding suitable control genes is essential for gene quantification. In this study, a genome‐wide survey of reference genes during metamorphism was performed on silkworm Bombyx mori. Twelve genes were chosen as putative reference genes based on a whole genome oligonucleotide microarray normalized by external controls. Then, qRT‐PCR was employed for further validation and selection of potential reference gene candidates. The results were analyzed, and stable genes were selected using geNorm 3.4 and NormFinder software. Finally, considering factors from every aspect, translation initiation factor 4A, translation initiation factor 3 subunit 4, and translation initiation factor 3 subunit 5 (represented by sw22934, swl4876, and swl3956) were selected as reliable internal controls across the examined developmental stages, while cytoplasmic actin (sw22671), the commonly used reference gene in a previous study was shown to vary drastically throughout the examined developmental stages. For future research, we recommend the use of the geometric mean of those three stable reference genes as an accurate normalization factor for data normalization of different developmental stages during metamorphism.
Url:
DOI: 10.1111/j.1744-7917.2008.00227.x
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Istex, to step Corpus: 000603
- to stream Istex, to step Curation: 000570
- to stream Istex, to step Checkpoint: 000157
- to stream Main, to step Merge: 001611
- to stream Main, to step Curation: 001607
Le document en format XML
<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">Reference genes identified in the silkworm Bombyx mori during metamorphism based on oligonucleotide microarray and confirmed by qRT‐PCR</title><author><name sortKey="Wang, Gen Ong" sort="Wang, Gen Ong" uniqKey="Wang G" first="Gen-Hong" last="Wang">Gen-Hong Wang</name></author><author><name sortKey="Xia, Qing Ou" sort="Xia, Qing Ou" uniqKey="Xia Q" first="Qing-You" last="Xia">Qing-You Xia</name></author><author><name sortKey="Cheng, Dao Un" sort="Cheng, Dao Un" uniqKey="Cheng D" first="Dao-Jun" last="Cheng">Dao-Jun Cheng</name></author><author><name sortKey="Duan, Jun" sort="Duan, Jun" uniqKey="Duan J" first="Jun" last="Duan">Jun Duan</name></author><author><name sortKey="Zhao, Ping" sort="Zhao, Ping" uniqKey="Zhao P" first="Ping" last="Zhao">Ping Zhao</name></author><author><name sortKey="Chen, Jie" sort="Chen, Jie" uniqKey="Chen J" first="Jie" last="Chen">Jie Chen</name></author><author><name sortKey="Zhu, Li" sort="Zhu, Li" uniqKey="Zhu L" first="Li" last="Zhu">Li Zhu</name></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:E2A351E4100C5023D8E964D986BEA645E7B0DBCA</idno><date when="2008" year="2008">2008</date><idno type="doi">10.1111/j.1744-7917.2008.00227.x</idno><idno type="url">https://api.istex.fr/ark:/67375/WNG-F0LXHWKL-F/fulltext.pdf</idno><idno type="wicri:Area/Istex/Corpus">000603</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">000603</idno><idno type="wicri:Area/Istex/Curation">000570</idno><idno type="wicri:Area/Istex/Checkpoint">000157</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Checkpoint">000157</idno><idno type="wicri:doubleKey">1672-9609:2008:Wang G:reference:genes:identified</idno><idno type="wicri:Area/Main/Merge">001611</idno><idno type="wicri:Area/Main/Curation">001607</idno><idno type="wicri:Area/Main/Exploration">001607</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main">Reference genes identified in the silkworm Bombyx mori during metamorphism based on oligonucleotide microarray and confirmed by qRT‐PCR</title><author><name sortKey="Wang, Gen Ong" sort="Wang, Gen Ong" uniqKey="Wang G" first="Gen-Hong" last="Wang">Gen-Hong Wang</name><affiliation wicri:level="1"><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Agriculture and Life Sciences, Chongqing University, Chongqing</wicri:regionArea><wicri:noRegion>Chongqing</wicri:noRegion></affiliation><affiliation wicri:level="1"><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Key Sericultural Laboratory of Agricultural Ministry, School of Biotechnology, Southwest University, Chongqing</wicri:regionArea><wicri:noRegion>Chongqing</wicri:noRegion></affiliation></author><author><name sortKey="Xia, Qing Ou" sort="Xia, Qing Ou" uniqKey="Xia Q" first="Qing-You" last="Xia">Qing-You Xia</name><affiliation wicri:level="1"><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Agriculture and Life Sciences, Chongqing University, Chongqing</wicri:regionArea><wicri:noRegion>Chongqing</wicri:noRegion></affiliation><affiliation wicri:level="1"><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Key Sericultural Laboratory of Agricultural Ministry, School of Biotechnology, Southwest University, Chongqing</wicri:regionArea><wicri:noRegion>Chongqing</wicri:noRegion></affiliation></author><author><name sortKey="Cheng, Dao Un" sort="Cheng, Dao Un" uniqKey="Cheng D" first="Dao-Jun" last="Cheng">Dao-Jun Cheng</name><affiliation wicri:level="1"><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Key Sericultural Laboratory of Agricultural Ministry, School of Biotechnology, Southwest University, Chongqing</wicri:regionArea><wicri:noRegion>Chongqing</wicri:noRegion></affiliation></author><author><name sortKey="Duan, Jun" sort="Duan, Jun" uniqKey="Duan J" first="Jun" last="Duan">Jun Duan</name><affiliation wicri:level="1"><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Agriculture and Life Sciences, Chongqing University, Chongqing</wicri:regionArea><wicri:noRegion>Chongqing</wicri:noRegion></affiliation><affiliation wicri:level="1"><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Key Sericultural Laboratory of Agricultural Ministry, School of Biotechnology, Southwest University, Chongqing</wicri:regionArea><wicri:noRegion>Chongqing</wicri:noRegion></affiliation></author><author><name sortKey="Zhao, Ping" sort="Zhao, Ping" uniqKey="Zhao P" first="Ping" last="Zhao">Ping Zhao</name><affiliation wicri:level="1"><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Key Sericultural Laboratory of Agricultural Ministry, School of Biotechnology, Southwest University, Chongqing</wicri:regionArea><wicri:noRegion>Chongqing</wicri:noRegion></affiliation></author><author><name sortKey="Chen, Jie" sort="Chen, Jie" uniqKey="Chen J" first="Jie" last="Chen">Jie Chen</name><affiliation wicri:level="1"><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Key Sericultural Laboratory of Agricultural Ministry, School of Biotechnology, Southwest University, Chongqing</wicri:regionArea><wicri:noRegion>Chongqing</wicri:noRegion></affiliation></author><author><name sortKey="Zhu, Li" sort="Zhu, Li" uniqKey="Zhu L" first="Li" last="Zhu">Li Zhu</name><affiliation wicri:level="1"><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Key Sericultural Laboratory of Agricultural Ministry, School of Biotechnology, Southwest University, Chongqing</wicri:regionArea><wicri:noRegion>Chongqing</wicri:noRegion></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Insect Science</title><title level="j" type="alt">INSECT SCIENCE</title><idno type="ISSN">1672-9609</idno><idno type="eISSN">1744-7917</idno><imprint><biblScope unit="vol">15</biblScope><biblScope unit="issue">5</biblScope><biblScope unit="page" from="405">405</biblScope><biblScope unit="page" to="413">413</biblScope><biblScope unit="page-count">9</biblScope><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><date type="published" when="2008-10">2008-10</date></imprint><idno type="ISSN">1672-9609</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1672-9609</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="Teeft" xml:lang="en"><term>Actin</term><term>Authors journal compilation institute</term><term>Bombyx</term><term>Bombyx mori</term><term>Candidate reference genes</term><term>Chinese academy</term><term>Control genes</term><term>Cytoplasmic</term><term>Cytoplasmic actin</term><term>Data normalization</term><term>Developmental stage</term><term>Developmental stages</term><term>Expression levels</term><term>Expression pattern</term><term>Expression stability</term><term>Fifth instar</term><term>Further validation</term><term>Gene</term><term>Gene expression normalization</term><term>Gene expression quantification</term><term>Genome</term><term>Genorm</term><term>Genorm software</term><term>Housekeeping genes</term><term>Insect science</term><term>Instar</term><term>Internal controls</term><term>Microarray</term><term>Mori</term><term>Mrna</term><term>Normalization</term><term>Normalization factor</term><term>Normfinder</term><term>Oligonucleotide microarray</term><term>Optimal number</term><term>Primer</term><term>Program normfinder</term><term>Proteasome beta subunit</term><term>Protein synthesis</term><term>Reference gene</term><term>Reference gene candidates</term><term>Reference genes</term><term>Ribosomal</term><term>Ribosomal protein</term><term>Ribosomal protein genes</term><term>Silkworm</term><term>Silkworm bombyx mori</term><term>Stable genes</term><term>Stable reference genes</term><term>Subunit</term><term>Translation initiation factor</term><term>Translation initiation factors</term><term>Wang</term><term>Zhang</term><term>Zoology</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Gene expression quantification at mRNA level is very important for post‐genomic studies, as gene expression level is the reflection of the special biological function of the target gene. Methods used for gene expression quantification, such as microarray or quantitative real‐time polymerase chain reaction (qRT‐PCR), require stable expressed reference genes. Thus, finding suitable control genes is essential for gene quantification. In this study, a genome‐wide survey of reference genes during metamorphism was performed on silkworm Bombyx mori. Twelve genes were chosen as putative reference genes based on a whole genome oligonucleotide microarray normalized by external controls. Then, qRT‐PCR was employed for further validation and selection of potential reference gene candidates. The results were analyzed, and stable genes were selected using geNorm 3.4 and NormFinder software. Finally, considering factors from every aspect, translation initiation factor 4A, translation initiation factor 3 subunit 4, and translation initiation factor 3 subunit 5 (represented by sw22934, swl4876, and swl3956) were selected as reliable internal controls across the examined developmental stages, while cytoplasmic actin (sw22671), the commonly used reference gene in a previous study was shown to vary drastically throughout the examined developmental stages. For future research, we recommend the use of the geometric mean of those three stable reference genes as an accurate normalization factor for data normalization of different developmental stages during metamorphism.</div></front></TEI><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Wang, Gen Ong" sort="Wang, Gen Ong" uniqKey="Wang G" first="Gen-Hong" last="Wang">Gen-Hong Wang</name></noRegion><name sortKey="Chen, Jie" sort="Chen, Jie" uniqKey="Chen J" first="Jie" last="Chen">Jie Chen</name><name sortKey="Cheng, Dao Un" sort="Cheng, Dao Un" uniqKey="Cheng D" first="Dao-Jun" last="Cheng">Dao-Jun Cheng</name><name sortKey="Duan, Jun" sort="Duan, Jun" uniqKey="Duan J" first="Jun" last="Duan">Jun Duan</name><name sortKey="Duan, Jun" sort="Duan, Jun" uniqKey="Duan J" first="Jun" last="Duan">Jun Duan</name><name sortKey="Wang, Gen Ong" sort="Wang, Gen Ong" uniqKey="Wang G" first="Gen-Hong" last="Wang">Gen-Hong Wang</name><name sortKey="Xia, Qing Ou" sort="Xia, Qing Ou" uniqKey="Xia Q" first="Qing-You" last="Xia">Qing-You Xia</name><name sortKey="Xia, Qing Ou" sort="Xia, Qing Ou" uniqKey="Xia Q" first="Qing-You" last="Xia">Qing-You Xia</name><name sortKey="Zhao, Ping" sort="Zhao, Ping" uniqKey="Zhao P" first="Ping" last="Zhao">Ping Zhao</name><name sortKey="Zhu, Li" sort="Zhu, Li" uniqKey="Zhu L" first="Li" last="Zhu">Li Zhu</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Sante/explor/CovidV2/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001607 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 001607 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Sante
|area= CovidV2
|flux= Main
|étape= Exploration
|type= RBID
|clé= ISTEX:E2A351E4100C5023D8E964D986BEA645E7B0DBCA
|texte= Reference genes identified in the silkworm Bombyx mori during metamorphism based on oligonucleotide microarray and confirmed by qRT‐PCR
}}
| This area was generated with Dilib version V0.6.33. |  |