MicroRNA (miRNA) gene expression profiling has provided important insights into plant and animal biology. However, there has not been ample published work about pitfalls associated with technical parameters in miRNA gene expression profiling. One source of pertinent information about technical variables in gene expression profiling is the separate and more well-established literature regarding mRNA expression profiling. However, many aspects of miRNA biochemistry are unique. For example, the cellular processing and compartmentation of miRNAs, the differential stability of specific miRNAs, and aspects of global miRNA expression regulation require specific consideration. Additional possible sources of systematic bias in miRNA expression studies include the differential impact of pre-analytical variables, substrate specificity of nucleic acid processing enzymes used in labeling and amplification, and issues regarding new miRNA discovery and annotation. We conclude that greater focus on technical parameters is required to bolster the validity, reliability, and cultural credibility of miRNA gene expression profiling studies.

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Published in Biochimica et Biophysica Acta -- Gene Regulatory Mechanisms, v. 1779, issue 11, p. 758-765.

Copyright © 2008 Elsevier B.V.

© 2008. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/.

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Funding Information

Funding was provided through NIH K08 NS050110 andNIH P30 49008400 (PTN), and the Kentucky Tobacco Research and Development Center (KTRDC), the USDA-NRI grants 2006-35301-17115 and 2006-35100-17433, the NSF MCB-0718029 (Subaward No. S-00000260), and the NIH 5 R03 AI 068934-02 (GT).