18S rRNA is a reliable normalisation gene for real time PCR based on influenza virus infected cells

Virology Journal

Volumn 9, Issue , 2012, Pages

  Kuchipudi, Suresh V ^a   Tellabati, Meenu ^a   Nelli, Rahul K ^a   White, Gavin A ^b   Perez, Belinda Baquero ^a   Sebastian, Sujith ^a   Slomka, Marek J ^c   Brookes, Sharon M ^c   Brown, Ian H ^c   Dunham, Stephen P ^a   Chang, Kin Chow ^a  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^b UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^c VETERINARY LABORATORIES AGENCY   (United Kingdom)

Author keywords

Data normalisation; H1N1; H2N3; H5N1; Housekeeping gene; Influenza A viruses; qRT PCR; Reference gene

Indexed keywords

BETA ACTIN; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE; RNA 18S;

ANIMAL CELL; ANIMAL EXPERIMENT; ARTICLE; BRONCHUS MUCOSA; CHICKEN; COMPUTER PROGRAM; CONTROLLED STUDY; GENE EXPRESSION; HOUSEKEEPING GENE; HUMAN; HUMAN CELL; INFLUENZA VIRUS; INFLUENZA VIRUS A; LUNG ALVEOLUS CELL; NONHUMAN; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SWINE; TRACHEA MUCOSA; VIRUS INFECTION;

ACTINS; ANIMALS; CELLS, CULTURED; CHICK EMBRYO; CHICKENS; DOGS; DUCKS; GENE EXPRESSION PROFILING; GENES, ESSENTIAL; GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASES; HUMANS; INFLUENZA A VIRUS; INFLUENZA A VIRUS, H1N1 SUBTYPE; INFLUENZA A VIRUS, H5N1 SUBTYPE; LUNG; REAL-TIME POLYMERASE CHAIN REACTION; REFERENCE STANDARDS; RESPIRATORY MUCOSA; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 18S; SOFTWARE; SWINE;

AVES; INFLUENZA A VIRUS; ORTHOMYXOVIRIDAE; SUIDAE;

EID: 84867037745     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-9-230     Document Type: Article

References (47)

1. Real-time QPCR normalisation; strategies and considerations. Huggett J, Dheda K, Bustin S, Zumla A, Genes and Immunity 2005 6 279 284 10.1038/sj.gene.6364190 15815687 (Pubitemid 40903399)
2. Quantification of mRNA using real-time reverse transcription (PCR QPCRx): trends and problems. Bustin SA, J Mol Endocrinol 2002 29 23 39 10.1677/jme.0.0290023 12200227 (Pubitemid 34965744)
3. Characterization of housekeeping genes in zebrafish: male-female differences and effects of tissue type, developmental stage and chemical treatment. McCurley A, Callard G, BMC Mol Biol 2008 9 102 10.1186/1471-2199-9- 102 19014500 (Pubitemid 352762899)
4. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. Bustin SA, J Mol Endocrinol 2000 25 169 193 10.1677/jme.0.0250169 11013345
5. Control selection for RNA quantitation. Suzuki T, Higgins PJ, Crawford DR, Biotechniques 2000 29 332 337 10948434 (Pubitemid 30658285)
6. Enhanced expression of a glyceraldehyde-3-phosphate dehydrogenase gene in human lung cancers. Tokunaga K, Nakamura Y, Sakata K, Fujimori K, Ohkubo M, Sawada K, Sakiyama S, Cancer Res 1987 47 5616 5619 3664468 (Pubitemid 18046754)
7. Increased glyceraldehyde-3-phosphate dehydrogenase gene expression in human pancreatic adenocarcinoma. Schek N, Hall BL, Finn OJ, Cancer Res 1988 48 6354 6359 3180054
8. Direct comparison of GAPDH, beta-actin, cyclophilin, and 28S rRNA as internal standards for quantifying RNA levels under hypoxia. Zhong H, Simons JW, Biochem Biophys Res Commun 1999 259 523 526 10.1006/bbrc.1999.0815 10364451 (Pubitemid 29335566)
9. Characterisation of mucosal lymphoid aggregates in ulcerative colitis: immune cell phenotype and TcR-gammadelta expression. Yeung MM, Melgar S, Baranov V, Oberg A, Danielsson A, Hammarstrom S, Hammarstrom ML, Gut 2000 47 215 227 10.1136/gut.47.2.215 10896913 (Pubitemid 30489765)
10. Utility of the housekeeping genes 18S rRNA, beta-actin and glyceraldehyde-3-phosphate-dehydrogenase for normalization in real-time quantitative reverse transcriptase-polymerase chain reaction analysis of gene expression in human T lymphocytes. Bas A, Forsberg G, Hammarstrom S, Hammarstrom ML, Scand J Immunol 2004 59 566 573 10.1111/j.0300-9475.2004.01440.x 15182252 (Pubitemid 38789226)
11. Degradation of cellular mRNA during influenza virus infection: its possible role in protein synthesis shutoff. Beloso A, Martinez C, Valcarcel J, Santaren JF, Ortin J, J Gen Virol 1992 73 Pt 3 575 581 1545220
12. The implications of using an inappropriate reference gene for real-time reverse transcription PCR data normalization. Dheda K, Huggett JF, Chang JS, Kim LU, Bustin SA, Johnson MA, Rook GA, Zumla A, Annal Biochem 2005 344 141 143 10.1016/j.ab.2005.05.022 (Pubitemid 41569389)
13. Reference gene selection for quantitative real-time PCR analysis in virus infected cells: SARS corona virus, Yellow fever virus, Human Herpesvirus-6, Camelpox virus and Cytomegalovirus infections. Radonic A, Thulke S, Bae HG, Muller MA, Siegert W, Nitsche A, Virol J 2005 2 7 10.1186/1743-422X-2-7 15705200 (Pubitemid 40404922)
14. An evaluation of potential reference genes for stability of expression in two salmonid cell lines after infection with either Piscirickettsia salmonis or IPNV. Pena AA, Bols NC, Marshall SH, BMC Res Notes 2010 3 101 10.1186/1756-0500-3-101 20398263
15. Determination of suitable housekeeping genes for normalisation of quantitative real time PCR analysis of cells infected with human immunodeficiency virus and herpes viruses. Watson S, Mercier S, Bye C, Wilkinson J, Cunningham AL, Harman AN, Virol J 2007 4 130 10.1186/1743-422X-4-130 18053162 (Pubitemid 351178235)
16. Using host 28S ribosomal RNA as a housekeeping gene for quantitative real-time reverse transcription-PCR (qRT-PCR) in virus-infected animal cells. Xue JL, Cheng XW, Curr Protoc Microbiol 2010 Chapter 1:Unit1D.2
17. Host gene expression profiling in influenza A virus-infected lung epithelial (A549) cells: a comparative analysis between highly pathogenic and modified H5N1 viruses. Chakrabarti A, Vipat V, Mukherjee S, Singh R, Pawar S, Mishra A, Virol J 2010 7 219 10.1186/1743-422X-7-219 20828378
18. Differential host gene responses in mice infected with two highly pathogenic avian influenza viruses of subtype H5N1 isolated from wild birds in Thailand. Hayashi T, Chaichoune K, Patchimasiri T, Hiromoto Y, Kawasaki Y, Wiriyarat W, Chakritbudsabong W, Prayoonwong N, Chaisilp N, Parchariyanon S, et al. Virology 2011 412 9 18 10.1016/j.virol.2010.12.040 21251691
19. Host immune-related gene responses against highly pathogenic avian influenza virus infection in vitro differ among chicken cell lines established from different organs. Watanabe C, Uchida Y, Ito H, Ito T, Saito T, Vet Immunol Immunopathol 2011 144 187 199 10.1016/j.vetimm.2011.10.002 22036867
20. Association of RIG-I with innate immunity of ducks to influenza. Barber MR, Aldridge JR Jr, Webster RG, Magor KE, Proc Natl Acad Sci U S A 2010 107 5913 5918 10.1073/pnas.1001755107 20308570
21. Gene expression signature-based screening identifies new broadly effective influenza a antivirals. Josset L, Textoris J, Loriod B, Ferraris O, Moules V, Lina B, N'guyen C, Diaz JJ, Rosa-Calatrava M, PLoS One 2010 5 10 13169 10.1371/journal.pone.0013169 20957181
22. Normalization of Real-Time Quantitative Reverse Transcription-PCR Data: A Model-Based Variance Estimation Approach to Identify Genes Suited for Normalization, Applied to Bladder and Colon Cancer Data Sets. Andersen CL, Jensen JL, rntoft TF, Cancer Res 2004 64 5245 5250 10.1158/0008-5472.CAN-04-0496 15289330 (Pubitemid 39006544)
23. Evolutionary rates vary among rRNA structural elements. Smit S, Widmann J, Knight R, Nucleic Acids Res 2007 35 3339 3354 10.1093/nar/gkm101 17468501 (Pubitemid 47073597)
24. Beta actin-an unsuitable internal control for RT-PCR. Selvey S, Thompson EW, Matthaei K, Lea RA, Irving MG, Griffiths LR, Mol Cell Probes 2001 15 307 311 10.1006/mcpr.2001.0376 11735303 (Pubitemid 33105000)
25. Ribosomal 18S RNA prevails over glyceraldehyde-3-phosphate dehydrogenase and beta-actin genes as internal standard for quantitative comparison of mRNA levels in invasive and noninvasive human melanoma cell subpopulations. Goidin D, Mamessier A, Staquet MJ, Schmitt D, Berthier-Vergnes O, Anal Biochem 2001 295 17 21 10.1006/abio.2001.5171 11476540 (Pubitemid 32721736)
26. Selection of appropriate control genes to assess expression of tumor antigens using real-time RT-PCR. Aerts JL, Gonzales MI, Topalian SL, Biotechniques 2004 36 84 1 14740490 (Pubitemid 38076385)
27. Validation of endogenous controls for gene expression analysis in microdissected human renal biopsies. Schmid H, Cohen CD, Henger A, Irrgang S, Schlondorff D, Kretzler M, Kidney Int 2003 64 356 360 10.1046/j.1523-1755.2003. 00074.x 12787429 (Pubitemid 36714191)
28. Preparation of cDNA and the generation of cDNA libraries: overview. Kimmel AR, Berger SL, Methods Enzymol 1987 152 307 316 3657577
29. mRNA and 18SôRNA coapplicationôreverse transcription for quantitative gene expression analysis. Lj Z, Altmann SW, Anal Biochem 2005 345 102 109 10.1016/j.ab.2005.07.028 16139233 (Pubitemid 41558200)
30. Cellular transcriptional profiling in influenza A virus-infected lung epithelial cells: the role of the nonstructural NS1 protein in the evasion of the host innate defense and its potential contribution to pandemic influenza. Geiss GK, Salvatore M, Tumpey TM, Carter VS, Wang X, Basler CF, Taubenberger JK, Bumgarner RE, Palese P, Katze MG, et al. Proc Natl Acad Sci U S A 2002 99 10736 10741 10.1073/pnas.112338099 12149435
31. Alteration of gene expression in human middle ear epithelial cells induced by influenza A virus and its implication for the pathogenesis of otitis media. Tong HH, Long JP, Li D, DeMaria TF, Microb Pathog 2004 37 193 204 10.1016/j.micpath.2004.06.012 15458780 (Pubitemid 39349043)
32. Integration of clinical data, pathology, and cDNA microarrays in influenza virus-infected pigtailed macaques (Macaca nemestrina). Baskin CR, Garcia-Sastre A, Tumpey TM, Bielefeldt-Ohmann H, Carter VS, Nistal-Villan E, Katze MG, J Virol 2004 78 10420 10432 10.1128/JVI.78.19.10420-10432.2004 15367608 (Pubitemid 39258367)
33. Analysis of gene-expression profiles by oligonucleotide microarray in children with influenza. Kawada J, Kimura H, Kamachi Y, Nishikawa K, Taniguchi M, Nagaoka K, Kurahashi H, Kojima S, Morishima T, J Gen Virol 2006 87 1677 1683 10.1099/vir.0.81670-0 16690933 (Pubitemid 43827222)
34. Differential gene-expression and host-response profiles against avian influenza virus within the chicken lung due to anatomy and airflow. Reemers SS, van Haarlem DA, Groot Koerkamp MJ, Vervelde L, J Gen Virol 2009 90 2134 2146 10.1099/vir.0.012401-0 19494054
35. Cellular host transcriptional responses to influenza A virus in chicken tracheal organ cultures differ from responses in in vivo infected trachea. Reemers SS, Groot Koerkamp MJ, Holstege FC, van Eden W, Vervelde L, Vet Immunol Immunopathol 2009
36. The effect of feed restriction on expression of hepatic lipogenic genes in broiler chickens and the function of SREBP1. Wang PH, Ko YH, Chin HJ, Hsu C, Ding ST, Chen CY, Comp Biochem Physiol B Biochem Mol Biol 2009 153 327 331 10.1016/j.cbpb.2009.04.003 19383549
37. Potential role of leptin in increase of fatty acid synthase gene expression in chicken liver. Dridi S, Buyse J, Decuypere E, Taouis M, Domest Anim Endocrinol 2005 29 646 660 10.1016/j.domaniend.2005.05.002 15941644 (Pubitemid 41415665)
38. The differential expression of hepatic genes between prelaying and laying geese. Ding ST, Yen CF, Wang PH, Lin HW, Hsu JC, Shen TF, Poult Sci 2007 86 1206 1212 17495093 (Pubitemid 47580996)
39. Reference gene selection for normalization of PCR analysis in chicken embryo fibroblast infected with H5N1 AIV. Yue H, Lei XW, Yang FL, Li MY, Tang C, Virol Sin 2010 25 425 431 10.1007/s12250-010-3114-4 21221921
40. Validation of endogenous reference genes for qRT-PCR analysis of human visceral adipose samples. Mehta R, Birerdinc A, Hossain N, Afendy A, Chandhoke V, Younossi Z, Baranova A, BMC Mol Biol 2010 11 39 10.1186/1471-2199-11-39 20492695
41. Genomic DNA standards for gene expression profiling in Mycobacterium tuberculosis. Talaat AM, Howard ST, Hale W, Lyons R, Garner H, Johnston SA, Nucleic Acids Res 2002 30 104 10.1093/nar/gnf103 12384606
42. Comparison of reverse transcriptases in gene expression analysis. Stahlberg A, Kubista M, Pfaffl M, Clin Chem 2004 50 1678 1680 10.1373/clinchem.2004.035469 15331507 (Pubitemid 39121243)
43. The replication-related organization of bacterial genomes. Rocha EP, Microbiology 2004 150 1609 1627 10.1099/mic.0.26974-0 15184548 (Pubitemid 38923661)
44. Accurate normalization of real-time quantitative QPCR data by geometric averaging of multiple internal controls. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F, Genome Biol 2002 3 34
45. Rapid death of duck cells infected with influenza: a potential mechanism for host resistance to H5N1. Kuchipudi SV, Dunham SP, Nelli R, White GA, Coward VJ, Slomka MJ, Brown IH, Chang KC, Immunol Cell Biol 2012 90 116 123 10.1038/icb.2011.17 21423263
46. Mammalian Innate Resistance to Highly Pathogenic Avian Influenza H5N1 Virus Infection is Mediated through Reduced Pro-inflammation and Infectious Virus Release. Nelli RK, Dunham SP, Kuchipudi SV, White GA, Baquero BP, Chang P, Ghaemmaghami A, Brookes S, Brown IH, Chang KC, J Virol 2012 86 17 9201 9210 10.1128/JVI.00244-12 22718824
47. Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper-Excel-based tool using pair-wise correlations. Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP, Biotechnol Lett 2004 26 509 515 15127793 (Pubitemid 38448421)