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RNA degradation compromises the reliability of microRNA expression profiling

Ibberson, David ; Benes, Vladimir ; Muckenthaler, Martina U. ; Castoldi, Mirco

In: BMC Biotechnology, 9 (2009), Nr. 102. pp. 1-9. ISSN 1472-6750

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Abstract

Background: MicroRNAs are small non-coding RNAs that post-transcriptionally regulate gene expression and their expression is frequently altered in human diseases, including cancer. To correlate clinically relevant parameters with microRNA expression, total RNA is frequently prepared from samples that were archived for various time periods in frozen tissue banks but, unfortunately, RNA integrity is not always preserved in these frozen tissues. Here, we investigate whether experimentally induced RNA degradation affects microRNA expression profiles. Results: Tissue samples were maintained on ice for defined time periods prior to total RNA extraction, which resulted in different degrees of RNA degradation. MicroRNA expression was then analyzed by microarray analysis (miCHIP) or microRNA-specific real-time quantitative PCR (miQPCR). Our results demonstrate that the loss of RNA integrity leads to in unpredictability of microRNA expression profiles for both, array-based and miQPCR assays. Conclusion: MicroRNA expression cannot be reliably profiled in degraded total RNA. For the profiling of microRNAs we recommend use of RNA samples with a RNA integrity number equal to or above seven.

Item Type: Article
Journal or Publication Title: BMC Biotechnology
Volume: 9
Number: 102
Publisher: BioMed Central
Place of Publication: London
Date Deposited: 09 Feb 2016 13:18
Date: 2009
ISSN: 1472-6750
Page Range: pp. 1-9
Faculties / Institutes: Service facilities > Cluster of Excellence Cellular Networks
Service facilities > European Molecular Biology Laboratory (EMBL)
Medizinische Fakultät Heidelberg > Universitätskinderklinik
Subjects: 570 Life sciences
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