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MicroRNA expression profiling using microarrays

Nature Protocols volume 3, pages 563–578 (2008)Cite this article

Abstract

Microarray technology is a powerful high-throughput tool capable of monitoring the expression of thousands of small noncoding RNAs at once within tens of samples processed in parallel in a single experiment. To conduct a genome-wide analysis of miRNA expression of normal and disease samples, such as cancer, and to distinguish expression signatures associated with diagnosis, prognosis and therapeutic interventions, we have developed a unique miRNA microarray assay on a CodeLink platform. The miRNA array consists of 4,104 probes printed in duplicate. This array can simultaneously profile more than 1,500 mature miRNAs and their corresponding precursors from 474 human and 373 mouse miRNA genes. The full protocol details of the miRNA microarray assay developed by our group are described here, including miRNA oligo probe design, array fabrication and miRNA target preparation (by reverse transcription of total RNA), target-probe hybridization on array, signal detection and data analysis. The assay is simple, can be easily standardized and allows the reproducible profiling of up to 24 total RNA samples within 24 h.

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Figure 1: Procedures and main steps of miRNA expression profiling.
Figure 2: miRNA oligo probe design and nomenclature of probe annotation.
Figure 3: Diagrams of detailed principle and procedure of miRNA expression profiling.
Figure 4: The QC image of version 4.0 miRNA array.
Figure 5: '4 × 8 miRNA version 4.0' printing parameters.
Figure 6: Programmed miRNA array hybridization protocol.
Figure 7: Diagrams of plates reformatting in oligo probe library construction.

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Acknowledgements

Dr. Calin is supported by the CLL Global Research Foundation and, in part, as a University of Texas System Regents Research Scholar and as a Fellow of The University of Texas MD Anderson Research Trust, and Drs. Liu and Croce are supported by Program Project Grants from the National Cancer Institute. We apologize to our colleagues whose work was not cited due to space limitations.

Author information

Author notes

  1. George Adrian Calin

    Present address: Present address: Department of Experimental Therapeutics & Department of Cancer Genetics, University of Texas, MD Anderson Cancer Center, Houston, Texas 77030, USA.,

  2. Chang-Gong Liu and George Adrian Calin: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Molecular Virology, Immunology and Medical Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, 43210, Ohio, USA

    Chang-Gong Liu, George Adrian Calin, Stefano Volinia & Carlo M Croce

  2. Morphology and Embryology Department, University of Ferrara, Ferrara, 44100, Italy

    Stefano Volinia

Authors
  1. Chang-Gong Liu
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  2. George Adrian Calin
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  3. Stefano Volinia
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  4. Carlo M Croce
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Corresponding author

Correspondence to Carlo M Croce.

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Liu, CG., Calin, G., Volinia, S. et al. MicroRNA expression profiling using microarrays. Nat Protoc 3, 563–578 (2008). https://doi.org/10.1038/nprot.2008.14

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