title: RNA degradation compromises the reliability of microRNA expression profiling.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Genomics Core Facility, EMBL, Meyerhofstrasse 1 D-69117 Heidelberg, Germany. ibberson@embl.de
authors.forename: David
authors.initials: D
authors.lastname: Ibberson
authors.forename: Vladimir
authors.initials: V
authors.lastname: Benes
authors.forename: Martina U
authors.initials: MU
authors.lastname: Muckenthaler
authors.forename: Mirco
authors.initials: M
authors.lastname: Castoldi
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D051379:Mice; D035683:MicroRNAs / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D020871:RNA Stability; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D035683:MicroRNAs