E-MTAB-1938 - microRNA profiling by array from pig cardiocirculatory tissues using a technique which allows detection of 10^-18 moles to 10^-14 moles of microRNAs in a linear range and allows for hybridisation quality control/reproducibility

Status
Released on 30 April 2014, last updated on 3 June 2014
Organism
Sus scrofa
Samples (20)
Array (1)
Protocols (7)
Description
The short length of miRNAs results in a high dynamic range of melting temperatures and therefore impedes a proper selection of detection probes or optimized PCR primers. While miRNA microarrays allow for massive parallel and accurate relative measurement of all known miRNAs, they have so far been less useful as an assay for absolute quantification. Here we developed a new method based not only to the hybridization process that presents the limits before described, but integrating the hybridization to an enzymatic reaction. Moreover we introduced spike-in in the hybridization-enzymatic reaction allowing the quantification of miRNAs respect to them, canceling biases related to sequence, labeling, or hybridization. An alternative method for the absolute miRNA quantization was recently proposed by Bissels (Absolute quantification of microRNAs by using a universal reference. RNA). It was based on the Absolute quantification of microRNAs by using a universal reference consisting of 954 synthetic human, mouse, rat, and viral miRNAs, with each individual oligoribonucleotide present in equimolar concentrations with tested miRNAs. Thereby, any single miRNA detected on a microarray can be quantified by directly comparing its signal intensity with the one obtained by the same miRNA sequence present in the universal reference adjusting for biases related to sequence, labeling, hybridization, or signal detection. Our method allowed the detection of a comparable concentration of miRNA (10^-18 moles to 10^-14 moles in a linear range), but allows controlling the hybridization quality and reproducibility basing on the results of the interpolation of the spike-in dependent curve. Moreover, our method does not influenced by phenomena imputable to different labeling process due to different sequences because labeling was due only to the incorporation of biotin-d(A) if the hybridized miRNA acted as primer for the klenow enzyme. This method allowed the discussion of miRNA genes expression in 9 different tissues relating them with tissue functionality in the cardiocirculatory system.
Experiment types
microRNA profiling by array, co-expression, in vivo, organism part comparison
Contact
Citation
Systems Biology approach to dissect the complexity of regulatory networks in S. scrofa Cardiocirculatory System. Paolo Martini, Gabriele Sales, Enrica Calura, Gerolamo Lanfranchi, Chiara Romualdi.
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-MTAB-1938.idf.txt
Sample and data relationshipE-MTAB-1938.sdrf.txt
Raw data (1)E-MTAB-1938.raw.1.zip
Processed data (1)E-MTAB-1938.processed.1.zip
Array designA-MEXP-2348.adf.txt
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