Abstract
Micro RNA (miRNAs) are a class of 17–25 nucleotides noncoding RNAs that have been shown to have critical functions in a wide variety of biological processes. Measuring quantity of miRNAs in tissues of different physiological and pathological conditions is an important first step to investigate the functions of miRNAs. To this date, the number of identified miRNA consists of around 850 different species, and more sequence-predicted miRNA genes are awaiting experimental confirmation. The need for high-throughput technologies allowing to profile all known miRNAs with power similar to microarray and precision/specificity of qPCR is evident. The example of such system based on high-density array of nanoliter PCR assays is described here. Functionally equivalent to a microtiter plate, a single OpenArray™ nanoplate makes possible to do up to 3,072 real-time PCRs at a single experiment. Methods for miRNA profiling using the dual-label probe chemistry (Taqman®) are outlined in this chapter, and experimental data illustrating system performance are provided.
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References
Nilsen TW (2007) Mechanisms of microRNA-mediated gene regulation in animal cells. Trends Genet, 23:243–249.
Ambros V (2004) The functions of animal microRNAs. Nature, 431:350–355.
Kloosterman WP, Plasterk RH (2006) The diverse functions of microRNAs in animal development and disease. Dev Cell, 11:441–450.
Hunter MP, Ismail N, Zhang X, Aguda BD, Lee EJ, Yu L, Xiao T, Schafer J, Lee ML, Schmittgen TD, Nana-Sinkam SP, Jarjoura D, Marsh CB (2008) Detection of microRNA expression in human peripheral blood microvesicles. PLoS, 3:e3694.
Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, Downing JR, Jacks T, Horvitz TH, Golub TR (2005) MicroRNA profiles classify human cancers. Nature, 435:834–838.
Vass L, Kelemen JZ, Feher LZ, Lorincz Z, Kulin S, Xseh S, Dorman G, Puskas LG (2009) Toxicogenomics screening of small molecules using high-density, nanocapillary real-time PCR. Int J Mol Med, 23:65–74.
Dixon JM, Lubomirski M, Amaratunga D, Morrison TB, Brenan CJ, Ilyin SE (2009) Nanoliter high-thorughput RT-qPCR: a statistical analysis and assessment. Biotechniques, 46:ii–viii.
Wang K, Zhang S, Marzolf B, Troisch P, Brightman A, Hu Z, Hood LE, Galas DJ (2009) Circulating miRNAs, potential biomarkers for drug-induced liver injury. Proc Natl Acad Sci USA, 11:4402–4407.
Williams AE, Larner-Svensson H, Perry MM, Campbell GA, Herrick SE, Adcock IM, Erjefalt JS, Chung KF, Lindsay MA (2009) MicroRNA expression profiling in mild asthmatic human airways and effect of corticosteroid therapy. PLoS, 4:e5889.
Sun Y, Koo S, White N, Peralta P, Esau C, Dean N, Perera RJ (2004) Development of a micro-array to detect human and mouse microRNAs and characterization of expression in human organs. Nucleic Acids Res, 32:e188.
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Grigorenko, E.V., Ortenberg, E., Hurley, J., Bond, A., Munnelly, K. (2011). miRNA Profiling on High-Throughput OpenArray™ System. In: Wu, W. (eds) MicroRNA and Cancer. Methods in Molecular Biology, vol 676. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-863-8_8
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DOI: https://doi.org/10.1007/978-1-60761-863-8_8
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Publisher Name: Humana Press, Totowa, NJ
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