Preferencje help
Widoczny [Schowaj] Abstrakt
Liczba wyników
2011 | 58 | 4 |
Tytuł artykułu

How the RNA isolation method can affect microRNA microarray results

Warianty tytułu
Języki publikacji
 The quality of RNA is crucial in gene expression experiments. RNA degradation interferes in the measurement of gene expression, and in this context, microRNA quantification can lead to an incorrect estimation. In the present study, two different RNA isolation methods were used to perform microRNA microarray analysis on porcine brain tissue. One method is a phenol-guanidine isothiocyanate-based procedure that permits isolation of total RNA. The second method, miRVana™ microRNA isolation, is column based and recovers the small RNA fraction alone. We found that microarray analyses give different results that depend on the RNA fraction used, in particular because some microRNAs appear very sensitive to the RNA isolation method. We conclude that precautions need to be taken when comparing microarray studies based on RNA isolated with different methods.
Opis fizyczny
  • Department of Basic Animal and Veterinary Sciences, Section of Genetics and Bioinformatics, Faculty of Life Sciences, University of Copenhagen, Copenhagen, Denmark
  • Accerbi M, Schmidt SA, De PE, Park S, Jeong DH, Green PJ (2010) Methods for isolation of total RNA to recover miRNAs and other small RNAs from diverse species. Methods Mol Biol 592: 31-50. 
  • Ach RA, Wang H, Curry B (2008) Measuring microRNAs: Comparisons of microarray and quantitative PCR measurements, and of different total RNA prep methods. BMC Biotechnol 8: 69. 
  • Becker C, Hammerle-Fickinger A, Riedmaier I, Pfaffl MW (2010) mRNA and microRNA quality control for RT-qPCR analysis. Methods 50: 237-243. 
  • Cloonan N, Brown MK, Steptoe AL, Wani S, Chan WL, Forrest AR, Kolle G, Gabrielli B, Grimmond SM (2008) The miR-17-5p microRNA is a key regulator of the G1/S phase cell cycle transition. Genome Biol 9: R127. 
  • Doleshal M, Magotra AA, Choudhury B, Cannon BD, Labourier E, Szafranska AE (2008) Evaluation and validation of total RNA extraction methods for microRNA expression analyses in formalin-fixed, paraffin-embedded tissues. J Mol Diagn 10: 203-211. 
  • Friedman RC, Kai-How Farh K, Burge BC, Bartel DP (2009) MicroRNAs: critical mediators of differentiation, development and disease. Genome Res 19: 92-105.
  • Hammerle-Fickinger A, Riedmaier I, Becker C, Meyer HH, Pfaffl MW, Ulbrich SE (2010) Validation of extraction methods for total RNA and miRNA from bovine blood prior to quantitative gene expression analyses. Biotechnol Lett 32: 35-44. 
  • Ibberson D, Benes V, Muckenthaler MU, Castoldi M (2009) RNA degradation compromises the reliability of microRNA expression profiling. BMC Biotechnol 9: 102. 
  • Liu A, Tetzlaff MT, Vanbelle P, Elder D, Feldman M, Tobias JW, Sepulveda AR, Xu X (2009) MicroRNA expression profiling outperforms mRNA expression profiling in formalin-fixed paraffin-embedded tissues. Int J Clin Exp Pathol 2: 519-527. 
  • Maouche S, Poirier O, Godefroy T, Olaso R, Gut I, Collet JP, Montalescot G, Cambien F (2008) Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells. BMC Genomics 9: 302. 
  • Masotti A, Caputo V, Da Sacco L, Pizzuti A, Dallapiccola B, Bottazzo GF (2009) Quantification of small non-coding RNAs allows an accurate comparison of miRNA expression profiles. J Biomedic Biotechnol 2009: 659028. 
  • Park SY, Lee JH, Ha M, Nam JW, Kim VN. (2009) miR-29 miRNAs activate p53 by targeting p85 alpha and CDC42. Nat Struct Mol Biol 16: 23-29. 
  • Sato F, Tsuchiya S, Terasawa K, Tsujimoto G (2009) Intra-platform repeatability and inter-platform comparability of microRNA microarray technology. PLoS One 4: e5540. 
  • Smyth GK, Michaud J, Scott HS (2005) Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 21: 2067-2075. 
  • Tian G, Yin XY, Luo H, Xu XH, Bolund L, Zhang XQ (2010) Sequencing bias: comparison of different protocols of MicroRNA library construction. BMC Biotechnol 10: 64. 
  • Wang WX, Wilfred BR, Baldwin DA, Isett RB, Ren N, Stromberg A, Nelson PT (2008) Focus on RNA isolation: obtaining RNA for microRNA (miRNA) expression profiling analyses of neural tissue. Biochim Biophys Acta 1779: 749-757. 
  • Zhang X, Chen J, Radcliffe T, Lebrun DP, Tron VA, Feilotter H (2008) An array-based analysis of microRNA expression comparing matched frozen and formalin-fixed paraffin-embedded human tissue samples. J Mol Diagn 10: 513-519. 
Typ dokumentu
Identyfikator YADDA
JavaScript jest wyłączony w Twojej przeglądarce internetowej. Włącz go, a następnie odśwież stronę, aby móc w pełni z niej korzystać.