Neurobiology of Aging
Volume 31, Issue 4 , Pages 654-664 , April 2010

Inter-age variability of bona fide unvaried transcripts: Normalization of quantitative PCR data in ischemic stroke

  • M.W. Sieber

      Affiliations

    • Department of Anaesthesiology and Intensive Care Medicine, University Hospital, Friedrich-Schiller University, 07743 Jena, Germany
    • Department of Neurology, University Hospital, Friedrich-Schiller University, 07743 Jena, Germany
    • For the ARGES consortium.
  • ,
  • M. Guenther

      Affiliations

    • Department of Neurology, University Hospital, Friedrich-Schiller University, 07743 Jena, Germany
  • ,
  • M. Kohl

      Affiliations

    • Department of Mathematical Statistics, University of Bayreuth, Bayreuth, Germany
  • ,
  • O.W. Witte

      Affiliations

    • Department of Neurology, University Hospital, Friedrich-Schiller University, 07743 Jena, Germany
    • For the ARGES consortium.
  • ,
  • R.A. Claus

      Affiliations

    • Department of Anaesthesiology and Intensive Care Medicine, University Hospital, Friedrich-Schiller University, 07743 Jena, Germany
    • For the ARGES consortium.
    • Corresponding Author InformationCorresponding author at: University Hospital, Friedrich-Schiller University, Erlanger Allee 101, D-07743 Jena, Germany. Tel.: +49 3641 9325860; fax: +49 3641 9325862.
  • ,
  • C. Frahm

      Affiliations

    • Department of Neurology, University Hospital, Friedrich-Schiller University, 07743 Jena, Germany
    • For the ARGES consortium.

Received 3 December 2007 ,Revised 12 May 2008 ,Accepted 25 May 2008.

References 

  1. Andersen CL, Jensen JL, Orntoft TF. 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
  2. Belayev L, Busto R, Zhao W, Fernandez G, Ginsberg MD. Middle cerebral artery occlusion in the mouse by intraluminal suture coated with poly-L-lysine: neurological and histological validation. Brain Res. 1999;833:181–190
  3. Bustin SA. Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems. J. Mol. Endocrinol. 2002;29:23–39
  4. Bustin SA, Nolan T. Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction. J. Biomol. Technol. 2004;15:155–166
  5. Carmichael ST. Rodent models of focal stroke: size, mechanism, and purpose. NeuroRx. 2005;2:396–409
  6. Coleman P, Finch C, Joseph J. The need for multiple time points in aging studies. Neurobiol. Aging. 2004;25:3–4
  7. de Kok JB, Roelofs RW, Giesendorf BA, Pennings JL, Waas ET, Feuth T, et al. Normalization of gene expression measurements in tumor tissues: comparison of 13 endogenous control genes. Lab Invest. 2005;85:154–159
  8. Forster MJ, Morris P, Sohal RS. Genotype and age influence the effect of caloric intake on mortality in mice. FASEB J. 2003;17:690–692
  9. Graven KK, McDonald RJ, Farber HW. Hypoxic regulation of endothelial glyceraldehyde-3-phosphate dehydrogenase. Am. J. Physiol. 1998;274:C347–C355
  10. Hamalainen HK, Tubman JC, Vikman S, Kyrola T, Ylikoski E, Warrington JA, et al. Identification and validation of endogenous reference genes for expression profiling of T helper cell differentiation by quantitative real-time RT-PCR. Anal. Biochem. 2001;299:63–70
  11. Harrison DC, Medhurst AD, Bond BC, Campbell CA, Davis RP, Philpott KL. The use of quantitative RT-PCR to measure mRNA expression in a rat model of focal ischemia – caspase-3 as a case study. Brain Res. Mol. Brain Res. 2000;75:143–149
  12. Hazell AS, Desjardins P, Butterworth RF. Increased expression of glyceraldehyde-3-phosphate dehydrogenase in cultured astrocytes following exposure to manganese. Neurochem. Int. 1999;35:11–17
  13. Huggett J, Dheda K, Bustin S, Zumla A. Real-time RT-PCR normalisation; strategies and considerations. Genes Immun. 2005;6:279–284
  14. Imai T, Seo H, Murata Y, Ohno M, Satoh Y, Funahashi H, et al. Adrenocorticotropin increases expression of c-fos and beta-actin genes in the rat adrenals. Endocrinology. 1990;127:1742–1747
  15. Ishitani R, Sunaga K, Hirano A, Saunders P, Katsube N, Chuang DM. Evidence that glyceraldehyde-3-phosphate dehydrogenase is involved in age-induced apoptosis in mature cerebellar neurons in culture. J. Neurochem. 1996;66:928–935
  16. Koizumi J, Nakazawa YY, Oneda TG. Experimental studies of ischemic brain edema 1 A new experimental model of cerebral embolism in ratsin which recirculation can be introduced in the ischemia area. Jpn. J. Stroke. 1986;8:1–8
  17. Lee CK, Weindruch R, Prolla TA. Gene-expression profile of the ageing brain in mice. Nat. Genet. 2000;25:294–297
  18. Longa EZ, Weinstein PR, Carlson S, Cummins R. Reversible middle cerebral artery occlusion without craniectomy in rats. Stroke. 1989;20:84–91
  19. Meisel C, Schwab JM, Prass K, Meisel A, Dirnagl U. Central nervous system injury-induced immune deficiency syndrome. Nat. Rev. Neurosci. 2005;6:775–786
  20. Ohl F, Jung M, Xu C, Stephan C, Rabien A, Burkhardt M, et al. Gene expression studies in prostate cancer tissue: which reference gene should be selected for normalization?. J Mol Med. 2005;83:1014–1124
  21. Pfaffl MW. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001;29:e45
  22. Rosamond W, Flegal K, Friday G, Furie K, Go A, Greenlund K, et al. Heart disease and stroke statistics – 2007 update: a report from the American heart association statistics committee and stroke statistics subcommittee. Circulation. 2007;115:e69–171
  23. Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 2000;132:365–386
  24. Sabath DE, Broome HE, Prystowsky MB. Glyceraldehyde-3-phosphate dehydrogenase mRNA is a major interleukin 2-induced transcript in a cloned T-helper lymphocyte. Gene. 1990;91:185–191
  25. Suzuki T, Higgins PJ, Crawford DR. Control selection for RNA quantitation. Biotechniques. 2000;29:332–337
  26. Tanaka R, Mochizuki H, Suzuki A, Katsube N, Ishitani R, Mizuno Y, et al. Induction of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) expression in rat brain after focal ischemia/reperfusion. J. Cereb. Blood Flow Metab. 2002;22:280–288
  27. Truelsen T, Ekman M, Boysen G. Cost of stroke in Europe. Eur J Neurol. 2005;12(Suppl 1):78–84
  28. Truelsen T, Piechowski-Jozwiak B, Bonita R, Mathers C, Bogousslavsky J, Boysen G. Stroke incidence and prevalence in Europe: a review of available data. Eur J Neurol. 2006;13:581–598
  29. Vandesompele, J., De Preter, K., Pattyn, F., Poppe, B., Van Roy, N., De Paepe, A., Speleman, F., 2002. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 3, RESEARCH0034.1–.11.
  30. Wolfe CD, Giroud M, Kolominsky-Rabas P, Dundas R, Lemesle M, Heuschmann P, et al. Variations in stroke incidence and survival in 3 areas of Europe. European Registries of Stroke (EROS) Collaboration. Stroke. 2000;31:2074–2079
  31. Yuan S, Rosenberg L, Ilieva A, Agapitos D, Duguid WP. Early changes of gene expression during cerulein supramaximal stimulation. Pancreas. 1999;19:45–50
  32. Zhong H, Simons JW. Direct comparison of GAPDH, beta-actin, cyclophilin, and 28S rRNA as internal standards for quantifying RNA levels under hypoxia. Biochem. Biophys. Res. Commun. 1999;259:523–526

PII: S0197-4580(08)00186-3

doi: 10.1016/j.neurobiolaging.2008.05.023

Neurobiology of Aging
Volume 31, Issue 4 , Pages 654-664 , April 2010