How the RNA isolation method can affect microRNA microarray results

Acta Biochimica Polonica

Volumn 58, Issue 4, 2011, Pages 535-540

  Podolska, Agnieszka ^a   Kaczkowski, Bogumil ^b   Litman, Thomas ^c   Fredholm, Merete ^a   Cirera, Susanna ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c LEO PHARMA A S   (Denmark)

Author keywords

Microarray; MicroRNA; MicroRNA isolation method; Pig; Small RNA fraction

Indexed keywords

SUIDAE; SUS;

EID: 84859926261     PISSN: 0001527X     EISSN: 1734154X     Source Type: Journal    
DOI: 10.18388/abp.2011_2221     Document Type: Article

References (17)

1. 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.
2. 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.
3. Becker C, Hammerle-Fickinger A, Riedmaier I, Pfaffl MW (2010) mRNA and microRNA quality control for RT-qPCR analysis. Methods 50: 237-243.
4. Cloonan N, Brown MK, Steptoe AL, Wani S, Chan WL, Forrest AR, Kolle G, Gabrielli B, Grimmond SM (2008) The miR-17-5p micro-RNA is a key regulator of the G1/S phase cell cycle transition. Genome Biol 9: R127.
5. Doleshal M, Magotra AA, Choudhury B, Cannot 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: 3.
6. Friedman RC, Kai-How Farh K, Burge BC, Bartel DP (2009) MicroRNAs: critical mediators of differentiation, development and disease. Genome Res 19: 92-105.
7. Hammerle-Fickinger A, Riedmaier I, Becker C, Meyer HHD, 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.
8. Ibberson D, Benes V, Muckenthaler MU, Castoldi M (2009) RNA degradation compromises the reliability of microRNA expression profiling. BMC Biotechnol 9: 102.
9. 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.
10. 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 Genom 9: 302.
11. Masotti A, Caputo V, Da Sacco L, Pizutti A, Dallapiccola B, Bottazo GF (2009) Quantication of small non-coding RNAs allows an accurate comparison of miRNA expression proles. J Biomedic Biotechnol 2009: 659028.
12. 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.
13. Sato F, Tsuchiya S, Terasawa K, Tsujimoto G (2009) Intra-platform repeatability and inter-platform comparability of microRNA microarray technology. PLoS One 4: e5540.
14. Smyth GK, Michaud J, Scott HS (2005) Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinform 21: 2067-2075.
15. 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.
16. 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.
17. 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.