An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues

doi:10.1073/pnas.0403293101

An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues

^*Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107; ^‡Compugen USA Inc., 7 Center Drive, Suite 9, Jamesburg, NJ 08831; ^§Department of Experimental and Diagnostic Medicine and Interdepartment Center for Cancer Research, University of Ferrara, Ferrara 44700, Italy; ^¶Diagnostics of Lymphoproliferative Diseases, National Institute of Cancer, Genoa 16123, Italy; and ^∥Laboratorio di Analisi Cliniche, Ospedale Civile di la Spezia, La Spezia 19126, Italy

Contributed by Carlo M. Croce, May 18, 2004

Abstract

MicroRNAs (miRNAs) are a class of small noncoding RNA genes recently found to be abnormally expressed in several types of cancer. Here, we describe a recently developed methodology for miRNA gene expression profiling based on the development of a microchip containing oligonucleotides corresponding to 245 miRNAs from human and mouse genomes. We used these microarrays to obtain highly reproducible results that revealed tissue-specific miRNA expression signatures, data that were confirmed by assessment of expression by Northern blots, real-time RT-PCR, and literature search. The microchip oligolibrary can be expanded to include an increasing number of miRNAs discovered in various species and is useful for the analysis of normal and disease states.

Footnotes

↵ ** To whom correspondence should be addressed. E-mail: c_croce{at}mail.jci.tju.edu.
↵ † C.-G.L. and G.A.C. contributed equally to this work.
Abbreviation: miRNA, microRNA.
Data deposition: The sequences reported in this paper have been deposited in the Array-Express database (accession nos. SAMPLE169150SUB621-SAMPLE169193SIUB621).