MiRNA profiling from freshly harvested duodenums and livers
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Mirco Castoldi
PROVIDER: E-GEOD-18788 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
RNA degradation compromises the reliability of microRNA expression profiling.
Ibberson David D Benes Vladimir V Muckenthaler Martina U MU Castoldi Mirco M
BMC biotechnology 20091221
<h4>Background</h4>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 in ...[more]
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Project description:Correlation of miRNA expression patterns with clinically relevant information is greatly facilitated by the retrospective analysis of samples archived in tissue banks. Unfortunately, the quality of samples stored in tissue banks is variable due to heterogeneity in pre-analytical preparation of clinical specimens. Collectively, these variables will impact the reliability of the results of the analysis. To date no systematic studies have been performed to investigate the relationship between total RNA degradation and miRNA profiles determined from snap-frozen collections or freshly harvested tissues. To investigate this question, we compared miRNA expression profiles generated through delaying the extraction of RNA from Liver and Duodenum, to generate different RNA integrities as defined by RIN values. Liver samples were collected from mice, sliced into five identical pieces, transfered into eppendorf tubes and either processed immediately (T0) or maintained on ice and at latter time points [30 min (T30), 60 min (T60), 120 min (T120) and 240 min (T240)]. RNA was extracted by using Trizol and RNA integrity was assessed by Bioanalyzer electropherograms. We found that liver samples did not show any significant RNA degradation even when samples remained on ice for up to 4 hrs However, miRNA expression profiling by microarray shows that miRNAs from freshly harvested Liver are partially degraded. Based on these data, we conclude that samples with low RIN values (less than 7) do not merit analysis on miRNA arrays.
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