An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues
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.
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MicroRNA expression has been predominantly characterized in tissues, with no comprehensive cellular studies.
“MicroRNA expression has been predominantly characterized in tissues, with no comprehensive cellular studies.”
From Toward the human cellular microRNAome (2017) · cites this paper as Liu et al. 2004
Cites
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Tili, E., Michaille, J.-J., Cimino, A., Costinean, S., Dumitru, C. D., Adair, B., Fabbri, M., Alder, H., Liu, C. G., Calin, G. A., et al. (2007) · The Journal of Immunology · doi:10.4049/jimmunol.179.8.5082 · Cited by 1,304 · see citing works
Self-citationA MicroRNA Signature of Hypoxia
Kulshreshtha, R., Ferracin, M., Wojcik, S. E., Garzon, R., Alder, H., Agosto-Perez, F. J., Davuluri, R., Liu, C.-G., Croce, C. M., Negrini, M., et al. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.01395-06 · Cited by 1,055 · see citing works
Self-citationMeng, F., Henson, R., Lang, M., Wehbe, H., Maheshwari, S., Mendell, J. T., Jiang, J., Schmittgen, T. D., & Patel, T. (2006) · Gastroenterology · doi:10.1053/j.gastro.2006.02.057 · Cited by 984 · see citing works
Regulation of miRNA expression during neural cell specification
Smirnova, L., Gräfe, A., Seiler, A., Schumacher, S., Nitsch, R., & Wulczyn, F. G. (2005) · European Journal of Neuroscience · doi:10.1111/j.1460-9568.2005.03978.x · Cited by 707 · see citing works
Markou, A., Tsaroucha, E. G., Kaklamanis, L., Fotinou, M., Georgoulias, V., & Lianidou, E. S. (2008) · Clinical Chemistry · doi:10.1373/clinchem.2007.101741 · Cited by 441 · see citing works
Interplay between miRNAs and human diseases
Paul, P., Chakraborty, A., Sarkar, D., Langthasa, M., Rahman, M., Bari, M., Singha, R. S., Malakar, A. K., & Chakraborty, S. (2018) · Journal of Cellular Physiology · doi:10.1002/jcp.25854 · Cited by 420 · see citing works
Toward the human cellular microRNAome
McCall, M. N., Kim, M.-S., Adil, M., Patil, A. H., Lu, Y., Mitchell, C. J., Leal-Rojas, P., Xu, J., Kumar, M., Dawson, V. L., et al. (2017) · Genome Research · doi:10.1101/gr.222067.117 · Cited by 151 · see citing works
Wang, H.-N., Crawford, B. M., Fales, A. M., Bowie, M. L., Seewaldt, V. L., & Vo-Dinh, T. (2016) · The Journal of Physical Chemistry C · doi:10.1021/acs.jpcc.6b03299 · Cited by 124 · see citing works
Everything you wanted to know about small RNA but were afraid to ask
Boyd, S. D. (2008) · Laboratory Investigation · doi:10.1038/labinvest.2008.32 · Cited by 108 · see citing works
HINCUTs in cancer: Hypoxia-induced noncoding ultraconserved transcripts
Ferdin, J., Nishida, N., Wu, X., Nicoloso, M. S., Shah, M. Y., Devlin, C., Ling, H., Shimizu, M., Kumar, K., Cortez, M. A., et al. (2013) · Cell Death & Differentiation · doi:10.1038/cdd.2013.119 · Cited by 103 · see citing works
Self-citationThe use of miRNA microarrays for the analysis of cancer samples with global miRNA decrease
Wu, D., Hu, Y., Tong, S., Williams, B. R. G., Smyth, G. K., & Gantier, M. P. (2013) · RNA · doi:10.1261/rna.035055.112 · Cited by 71 · see citing works
Expression of miR-15/107 Family MicroRNAs in Human Tissues and Cultured Rat Brain Cells
Wang, W.-X., Danaher, R. J., Miller, C. S., Berger, J. R., Nubia, V. G., Wilfred, B. S., Neltner, J. H., Norris, C. M., & Nelson, P. T. (2014) · Genomics, Proteomics & Bioinformatics · doi:10.1016/j.gpb.2013.10.003 · Cited by 67 · see citing works
- Authors
- Liu, C.-G., Calin, G. A., Meloon, B., Gamliel, N., Sevignani, C., Ferracin, M., Dumitru, C. D., Shimizu, M., Zupo, S., Dono, M., Alder, H., Bullrich, F., Negrini, M., & Croce, C. M.
- Affiliations
- 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
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2004-06-21
- Volume
- 101
- Issue
- 26
- Pages
- 9740-9744
- ISSN
- 0027-8424
- 1091-6490
- Cited by
- 778
- References
- 1
- Language
- en
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