Nucleic Acids Research Advance Access published online on March 13, 2007
Nucleic Acids Research, doi:10.1093/nar/gkl1118
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Methods Online |
A novel microarray approach reveals new tissue-specific signatures of known and predicted mammalian microRNAs
Novartis Institutes for BioMedical Research, Genome and Proteome Sciences, CH-4002 Basel, Switzerland, 1Friedrich Miescher Institute for Biomedical Research, PO Box 2543, CH-4002 Basel, Switzerland and 2Novartis Pharma AG, Biomarker Development, CH-4002 Basel, Switzerland
*To whom correspondence should be addressed. Tel: +49-61 3246142; Fax: +41-61-3242217; Email: jan.weiler{at}novartis.com Correspondence may also be addressed to Witold Filipowicz. Tel: +41-61 6974128; Fax: +41-61-6973976; E-mail: witold.filipowicz{at}fmi.ch
Received August 8, 2006. Revised October 30, 2006. Accepted February 27, 2007.
Microarrays to examine the global expression levels of microRNAs (miRNAs) in a systematic in-parallel manner have become important tools to help unravel the functions of miRNAs and to understand their roles in RNA-based regulation and their implications in human diseases. We have established a novel miRNA-specific microarray platform that enables the simultaneous expression analysis of both known and predicted miRNAs obtained from human or mouse origin. Chemically modified 2'-O-(2-methoxyethyl)-(MOE) oligoribonucleotide probes were arrayed onto Evanescent Resonance (ER) microchips by robotic spotting. Supplementing the complementary probes against miRNAs with carefully designed mismatch controls allowed for accurate sequence-specific determination of miRNA expression profiles obtained from a panel of mouse tissues. This revealed new expression signatures of known miRNAs as well as of novel miRNAs previously predicted using bioinformatic methods. Systematic confirmation of the array data with northern blotting and, in particular, real-time PCR suggests that the described microarray platform is a powerful tool to analyze miRNA expression patterns with rapid throughput and high fidelity.
The two authors have contributed equally to this work Present address: Fabrice A. Kolb, Protease Platform, Novartis Institutes for Biomedical Research, CH-4002 Basel, Switzerland Jonathan Hall, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland
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