Evaluation of potential reference genes for relative quantification by RT- qPCR in different porcine tissues derived from feeding studies

International Journal of Molecular Sciences

Volumn 12, Issue 3, 2011, Pages 1727-1734

  Li, Qimeng ^a   Domig, Konrad Johann ^a   Ettle, Thomas ^a   Windisch, Wilhelm ^b   Mair, Christiane ^a   Schedle, Karl ^a  

^a UNIVERSITY OF NATURAL RESOURCES AND LIFE SCIENCES   (Austria)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

Gene stability; Reference genes; RT qPCR; Sus scrofa

Indexed keywords

BETA ACTIN; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; HISTONE H3; RNA 18S; UBIQUITIN; ACTIN; HISTONE; RIBOSOME RNA; RNA;

ABDOMINAL FAT; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; FEEDING BEHAVIOR; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENETIC STABILITY; GENETIC VARIABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA EXTRACTION; SWINE; TISSUE CHARACTERIZATION; TISSUE TYPES; ANIMAL; GENETICS; KIDNEY; LIVER; METABOLISM; RNA STABILITY; STANDARD; STANDARDS; THYROID GLAND;

SUIDAE; SUS; SUS SCROFA;

ABDOMINAL FAT; ACTINS; ANIMALS; GENE EXPRESSION; GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (PHOSPHORYLATING); HISTONES; KIDNEY; LIVER; REFERENCE STANDARDS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA; RNA STABILITY; RNA, RIBOSOMAL; SWINE; THYROID GLAND; UBIQUITIN;

EID: 79953310768     PISSN: None     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms12031727     Document Type: Article

References (33)

1. EFSA. Opinion of the Scientific Panel on additives and products or substances used in animal feed (FEEDAP) on the use of iodine in feedingstuffs. EFSA J. 2005, 3, 1-42.
2. Schone, F.; Zimmermann, C.; Quanz, G.; Richter, G.; Leiterer, M. A high dietary iodine increases thyroid iodine stores and iodine concentration in blood serum but has little effect on muscle iodine content in pigs. Meat Sci. 2006, 72, 365-372.
3. Wagner, V.W.W.; Swoboda, S.; Ettle, T. Effects of varying dietary iodine supplementation as iodide or iodate on zootechnical performance, carcass quality and iodine concentrations in tissues of fattening pigs. Proc. Soc. Nutr. Physiol. 2008, 17, 59.
4. Hibbeler, S.; Scharsack, J.P.; Becker, S. Housekeeping genes for quantitative expression studies in the three-spined stickleback Gasterosteus aculeatus. BMC Mol. Biol. 2008, 9, 18.
5. Pfaffl, M.W.; Tichopad, A.; Prgomet, C.; Neuvians, T.P. Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper-Excel-based tool using pair-wise correlations. Biotechnol. Lett. 2004, 26, 509-515.
6. Brunner, A.M.; Yakovlev, I.A.; Strauss, S.H. Validating internal controls for quantitative plant gene expression studies. BMC Plant Biol. 2004, 4, 14.
7. Aerts, J.L.; Gonzales, M.I.; Topalian, S.L. Selection of appropriate control genes to assess expression of tumor antigens using real-time RT-PCR. Biotechniques 2004, 36, 84-91.
8. Zhang, Q.J.; Chadderton, A.; Clark, R.L.; Augustine-Rauch, K.A. Selection of normalizer genes in conducting relative gene expression analysis of embryos. Birth Defects Res. A Clin. Mol. Teratol. 2003, 67, 533-544.
9. Loseke, S.; Grage-Griebenow, E.; Wagner, A.; Gehlhar, K.; Bufe, A. Differential expression of IFN-alpha subtypes in human PBMC: Evaluation of novel real-time PCR assays. J. Immunol. Methods 2003, 276, 207-222.
10. Kim, B.R.; Nam, H.Y.; Kim, S.U.; Kim, S.I.; Chang, Y.J. Normalization of reverse transcription quantitative-PCR with housekeeping genes in rice. Biotechnol. Lett. 2003, 25, 1869-1872.
11. Sturzenbaum, S.R.; Kille, P. Control genes in quantitative molecular biological techniques: the variability of invariance. Comp. Biochem. Physiol. Part B Biochem. Mol. Biol. 2001, 130, 281-289.
12. Bustin, S.A. Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems. J. Mol. Endocrinol. 2002, 29, 23-39.
13. Matrisian, L.M.; Glaichenhaus, N.; Gesnel, M.C.; Breathnach, R. Epidermal growth factor and oncogenes induce transcription of the same cellular mRNA in rat fibroblasts. EMBO J. 1985, 4, 1435-1440.
14. Iovanna, J.L.; Dusetti, N.; Cadenas, B.; Calvo, E.L. Changes in growth and pancreatic mRNA concentrations during postnatal development of rat pancreas. Pancreas 1990, 5, 421-426.
15. Kanayama, S.; Liddle, R.A. Influence of food deprivation on intestinal cholecystokinin and somatostatin. Gastroenterology 1991, 100, 909-915.
16. Goldsworthy, S.M.; Goldsworthy, T.L.; Sprankle, C.S.; Butterworth, B.E. Variation in expression of genes used for normalization of Northern blots after induction of cell proliferation. Cell Prolif. 1993, 26, 511-518.
17. Moshier, J.A.; Cornell, T.; Majumdar, A.P. Expression of protease genes in the gastric mucosa during aging. Exp. Gerontol. 1993, 28, 249-258.
18. Hodin, R.A.; Chamberlain, S.M.; Meng, S. Pattern of rat intestinal brush-border enzyme gene expression changes with epithelial growth state. Am. J. Physiol. 1995, 269, C385-C391.
19. Yamada, H.C.D.; Monstein, H.J.; Hakanson, R. Effects of fasting on the expression of gastrin, cholecystokinin, and somatostatin genes and of various housekeeping genes in the pancreas and upper digestive tract of rats. Biochem. Biophys. Res. Commun. 1997, 231, 835-838.
20. Foss, D.L.; Baarsch, M.J.; Murtaugh, M.P. Regulation of hypoxanthine phosphoribosyltransferase, glyceraldehyde-3-phosphate dehydrogenase and beta-actin mRNA expression in porcine immune cells and tissues. Anim. Biotechnol. 1998, 9, 67-78.
21. Bustin, S.A.; Benes, V.; Garson, J.A.; Hellemans, J.; Huggett, J.; Kubista, M.; Mueller, R.; Nolan, T.; Pfaffl, M.W.; Shipley, G.L.; Vandesompele, J.; Wittwer, C.T. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin. Chem. 2009, 55, 611-622.
22. Vandesompele, J.; de Preter, K.; Pattyn, F.; Poppe, B.; van Roy, N.; de Paepe, A.; Speleman, F. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002, 3, research0034:1-research0034:11.
23. Garcia-Crespo, D.; Juste, R.A.; Hurtado, A. Selection of ovine housekeeping genes for normalisation by real-time RT-PCR; analysis of PrP gene expression and genetic susceptibility to scrapie. BMC Vet. Res. 2005, 1, 3.
24. Nygard, A.B.; Jorgensen, C.B.; Cirera, S.; Fredholm, M. Selection of reference genes for gene expression studies in pig tissues using SYBR green qPCR. BMC Mol. Biol. 2007, 8, 67.
25. Skovgaard, K.; Mortensen, S.; Poulsen, K.T.; Angen, O.; Heegaard, P.M. Validation of putative reference genes for qRT-PCR normalization in tissues and blood from pigs infected with Actinobacillus pleuropneumoniae. Vet. Immunol. Immunopathol. 2007, 118, 140-146.
26. Svobodova, K.; Bilek, K.; Knoll, A. Verification of reference genes for relative quantification of gene expression by real-time reverse transcription PCR in the pig. J. Appl. Genet. 2008, 49, 263-265.
27. Bustin, S.A. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J. Mol. Endocrinol. 2000, 25, 169-193.
28. Schmittgen, T.D.; Zakrajsek, B.A.; Mills, A.G.; Gorn, V.; Singer, M.J.; Reed, M.W. Quantitative reverse transcription-polymerase chain reaction to study mRNA decay: comparison of endpoint and real-time methods. Anal. Biochem. 2000, 285, 194-204.
29. Fleige, S.; Pfaffl, M.W. RNA integrity and the effect on the real-time qRT-PCR performance. Mol. Asp. Med. 2006, 27, 126-139.
30. Fleige, S.; Preissinger, W.; Meyer, H.H.; Pfaffl, M.W. The immunomodulatory effect of lactulose on Enterococcus faecium fed preruminant calves. J. Anim. Sci. 2009, 87, 1731-1738.
31. Schedle, K.; Pfaffl, M.W.; Plitzner, C.; Meyer, H.H.; Windisch, W. Effect of insoluble fibre on intestinal morphology and mRNA expression pattern of inflammatory, cell cycle and growth marker genes in a piglet model. Arch. Anim. Nutr. 2008, 62, 427-438.
32. Pfaffl, M.W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001, 29, e45.
33. Andersen, C.L.; Jensen, J.L.; Orntoft, T.F. 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. Cancer Res. 2004, 64, 5245-5250.