Validation of housekeeping genes as internal controls for studying gene expression during Pacific oyster (Crassostrea gigas) development by quantitative real-time PCR
Hatchery-reared larvae of the Pacific oyster (Crassostrea gigas) often suffer from massive mortality induced by Ostreid herpesvirus 1 (OsHV-1) infection, indicating the importance of better understanding of oyster immune defense systems. The accuracy of measurements of gene expression levels based o...
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ftchinacasciocas:oai:ir.qdio.ac.cn:337002/16729 2023-05-15T15:58:32+02:00 Validation of housekeeping genes as internal controls for studying gene expression during Pacific oyster (Crassostrea gigas) development by quantitative real-time PCR Du, Yishuai Zhang, Linlin Xu, Fei Huang, Baoyu Zhang, Guofan Li, Li Zhang, GF 2013-03-01 http://ir.qdio.ac.cn/handle/337002/16729 https://doi.org/10.1016/j.fsi.2012.12.007 英语 eng FISH & SHELLFISH IMMUNOLOGY Du, Yishuai; Zhang, Linlin; Xu, Fei; Huang, Baoyu; Zhang, Guofan; Li, Li.Validation of housekeeping genes as internal controls for studying gene expression during Pacific oyster (Crassostrea gigas) development by quantitative real-time PCR,FISH & SHELLFISH IMMUNOLOGY,2013,34(3):939-945 http://ir.qdio.ac.cn/handle/337002/16729 doi:10.1016/j.fsi.2012.12.007 6 Internal Control Real-time Pcr Ostreid Herpesvirus 1 Development Larva Fisheries Immunology Marine & Freshwater Biology Veterinary Sciences Science & Technology Life Sciences & Biomedicine NORMAL HUMAN TISSUES RT-PCR QUANTIFICATION COMPENDIUM HEMOCYTES ISOFORMS HOMOLOG HYPOXIA STRESS FRANCE Article 期刊论文 2013 ftchinacasciocas https://doi.org/10.1016/j.fsi.2012.12.007 2022-06-27T05:35:47Z Hatchery-reared larvae of the Pacific oyster (Crassostrea gigas) often suffer from massive mortality induced by Ostreid herpesvirus 1 (OsHV-1) infection, indicating the importance of better understanding of oyster immune defense systems. The accuracy of measurements of gene expression levels based on quantitative real-time PCR assays relies on the use of housekeeping genes as internal controls; however, few studies have focused on the selection of such internal controls. In this study, we conducted a comprehensive investigation of internal control genes during oyster development in virus-infected and uninfected samples. Transcriptome data for 38 developmental stages were downloaded and the gene expression patterns were classified into 30 clusters. A total of 317 orthologs of classical housekeeping genes in the oyster genome were annotated. After combining the expression profiles and oyster housekeeping gene dataset, 14 candidate internal controls were selected for further investigation: Elongation factor-1 alpha (EF-1 alpha), 18S rRNA (18S), 28S rRNA (28S), Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), beta-actin (ACT), Ribosomal protein L7 (RL7), Ribosomal protein L27 (RL27), Ribosomal protein L36 (RL36), Ribosomal protein S18 (RS18), Heterogeneous nuclear ribonucleoprotein A2/B1 (RO21), Eukaryotic translation elongation factor 2 (EF2), Ubiquitin-conjugating enzyme E2D2 (UBCD1), S-phase kinase-associated protein 1 (SKP1) and Heterogeneous nuclear ribonucleoprotein Q (HNRPQ). RNA was extracted from oyster larvae infected with OsHV-1 (group A; GA), and OsHV-1 free larvae (group B; GB). The expression levels of the 14 candidate internal controls were studied in GA and GB larvae by real-time PCR. Their expression stabilities were further analyzed using the GeNorm program. RL7 and RS18 were the most stable genes in both OsHV-1 infected (GA) and uninfected (GB) larvae. These results suggest that RL7 and RS18 could be used as internal controls for studying gene expression in normal growing oyster larvae and in ... Article in Journal/Newspaper Crassostrea gigas Pacific oyster Institute of Oceanology, Chinese Academy of Sciences: IOCAS-IR Pacific Fish & Shellfish Immunology 34 3 939 945 |
institution |
Open Polar |
collection |
Institute of Oceanology, Chinese Academy of Sciences: IOCAS-IR |
op_collection_id |
ftchinacasciocas |
language |
English |
topic |
Internal Control Real-time Pcr Ostreid Herpesvirus 1 Development Larva Fisheries Immunology Marine & Freshwater Biology Veterinary Sciences Science & Technology Life Sciences & Biomedicine NORMAL HUMAN TISSUES RT-PCR QUANTIFICATION COMPENDIUM HEMOCYTES ISOFORMS HOMOLOG HYPOXIA STRESS FRANCE |
spellingShingle |
Internal Control Real-time Pcr Ostreid Herpesvirus 1 Development Larva Fisheries Immunology Marine & Freshwater Biology Veterinary Sciences Science & Technology Life Sciences & Biomedicine NORMAL HUMAN TISSUES RT-PCR QUANTIFICATION COMPENDIUM HEMOCYTES ISOFORMS HOMOLOG HYPOXIA STRESS FRANCE Du, Yishuai Zhang, Linlin Xu, Fei Huang, Baoyu Zhang, Guofan Li, Li Zhang, GF Validation of housekeeping genes as internal controls for studying gene expression during Pacific oyster (Crassostrea gigas) development by quantitative real-time PCR |
topic_facet |
Internal Control Real-time Pcr Ostreid Herpesvirus 1 Development Larva Fisheries Immunology Marine & Freshwater Biology Veterinary Sciences Science & Technology Life Sciences & Biomedicine NORMAL HUMAN TISSUES RT-PCR QUANTIFICATION COMPENDIUM HEMOCYTES ISOFORMS HOMOLOG HYPOXIA STRESS FRANCE |
description |
Hatchery-reared larvae of the Pacific oyster (Crassostrea gigas) often suffer from massive mortality induced by Ostreid herpesvirus 1 (OsHV-1) infection, indicating the importance of better understanding of oyster immune defense systems. The accuracy of measurements of gene expression levels based on quantitative real-time PCR assays relies on the use of housekeeping genes as internal controls; however, few studies have focused on the selection of such internal controls. In this study, we conducted a comprehensive investigation of internal control genes during oyster development in virus-infected and uninfected samples. Transcriptome data for 38 developmental stages were downloaded and the gene expression patterns were classified into 30 clusters. A total of 317 orthologs of classical housekeeping genes in the oyster genome were annotated. After combining the expression profiles and oyster housekeeping gene dataset, 14 candidate internal controls were selected for further investigation: Elongation factor-1 alpha (EF-1 alpha), 18S rRNA (18S), 28S rRNA (28S), Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), beta-actin (ACT), Ribosomal protein L7 (RL7), Ribosomal protein L27 (RL27), Ribosomal protein L36 (RL36), Ribosomal protein S18 (RS18), Heterogeneous nuclear ribonucleoprotein A2/B1 (RO21), Eukaryotic translation elongation factor 2 (EF2), Ubiquitin-conjugating enzyme E2D2 (UBCD1), S-phase kinase-associated protein 1 (SKP1) and Heterogeneous nuclear ribonucleoprotein Q (HNRPQ). RNA was extracted from oyster larvae infected with OsHV-1 (group A; GA), and OsHV-1 free larvae (group B; GB). The expression levels of the 14 candidate internal controls were studied in GA and GB larvae by real-time PCR. Their expression stabilities were further analyzed using the GeNorm program. RL7 and RS18 were the most stable genes in both OsHV-1 infected (GA) and uninfected (GB) larvae. These results suggest that RL7 and RS18 could be used as internal controls for studying gene expression in normal growing oyster larvae and in ... |
format |
Article in Journal/Newspaper |
author |
Du, Yishuai Zhang, Linlin Xu, Fei Huang, Baoyu Zhang, Guofan Li, Li Zhang, GF |
author_facet |
Du, Yishuai Zhang, Linlin Xu, Fei Huang, Baoyu Zhang, Guofan Li, Li Zhang, GF |
author_sort |
Du, Yishuai |
title |
Validation of housekeeping genes as internal controls for studying gene expression during Pacific oyster (Crassostrea gigas) development by quantitative real-time PCR |
title_short |
Validation of housekeeping genes as internal controls for studying gene expression during Pacific oyster (Crassostrea gigas) development by quantitative real-time PCR |
title_full |
Validation of housekeeping genes as internal controls for studying gene expression during Pacific oyster (Crassostrea gigas) development by quantitative real-time PCR |
title_fullStr |
Validation of housekeeping genes as internal controls for studying gene expression during Pacific oyster (Crassostrea gigas) development by quantitative real-time PCR |
title_full_unstemmed |
Validation of housekeeping genes as internal controls for studying gene expression during Pacific oyster (Crassostrea gigas) development by quantitative real-time PCR |
title_sort |
validation of housekeeping genes as internal controls for studying gene expression during pacific oyster (crassostrea gigas) development by quantitative real-time pcr |
publishDate |
2013 |
url |
http://ir.qdio.ac.cn/handle/337002/16729 https://doi.org/10.1016/j.fsi.2012.12.007 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_relation |
FISH & SHELLFISH IMMUNOLOGY Du, Yishuai; Zhang, Linlin; Xu, Fei; Huang, Baoyu; Zhang, Guofan; Li, Li.Validation of housekeeping genes as internal controls for studying gene expression during Pacific oyster (Crassostrea gigas) development by quantitative real-time PCR,FISH & SHELLFISH IMMUNOLOGY,2013,34(3):939-945 http://ir.qdio.ac.cn/handle/337002/16729 doi:10.1016/j.fsi.2012.12.007 |
op_rights |
6 |
op_doi |
https://doi.org/10.1016/j.fsi.2012.12.007 |
container_title |
Fish & Shellfish Immunology |
container_volume |
34 |
container_issue |
3 |
container_start_page |
939 |
op_container_end_page |
945 |
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1766394280678522880 |