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miRNA Profiling
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The PMGC currently offers microRNA (miRNA) profiling services on the Agilent or NanoString platforms. Not sure which platform is best suited to your experimental needs? Click here.

miRBase is a public miRNA database created by the Wellcome Trust Sanger Institute. miRBase incorporates the database and gene naming roles, and contains 3 main sections including miRBase Sequences (all published miRNA sequences, genomic locations and associated annotation), miRBase Targets (a database of predicted miRNA target genes), and miRBase Registry (confidential service assigning official names for novel miRNA genes prior to publication of their discovery).


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What are miRNAs?

miRNA is regulatory RNA found in plants, nematodes and animals. miRNAs have been implicated as regulators of developmental timing, neuronal differentiation, cell proliferation, programmed cell death, fat metabolism, viral infections, and cancer. In mammals, microRNAs are thought to act as post-transcriptional modulators of gene expression.

What is “mature” miRNA?

miRNA occur in three different forms: long pri-miRNA, hairpin pre-miRNA, and short mature miRNA. In the nucleus, pri-miRNA is cleaved by the nuclease Drosha to form pre-miRNA. Pre-miRNA is 70-125 nucleotides long and form hairpin structures with an overhang of 2 nucleotides at the 3’ end. Pre-miRNA is exported into the cytoplasm by RanGTP and exportin5 proteins. In the cytoplasm, pre-miRNA is processed by the Dicer ribonuclease to form the mature miRNA. Mature miRNA are 19-23 nucleotides long.

Why profile miRNA expression?

As with protein-coding mRNA, a key to understanding the role of miRNA is to determine when and where they are expressed. The goal of profiling miRNA expression is to discover the specific mRNA molecules regulated by each miRNA molecule.

What are the challenges of using microarrays to profile miRNAs?

Microarrays are a good method for high-throughput expression profiling; however, one of the challenges of profiling miRNA expression is that the small size of the miRNA entities leaves little room for labelling or designing specific probes. Another challenge is the fact that miRNA exists in three forms (pri-miRNA, hairpin pre-miRNA and short mature miRNA). Expression profiling of short mature miRNA will require that signal from hairpin pre-miRNA and pri-miRNA can be eliminated. In addition, microarrays made with standard DNA probes are often unable to distinguish single nucleotides. Despite these challenges, researchers have successfully used microarrays to profile miRNA expression.

What are the features on Agilent’s miRNA microarray?

Agilent has 3 types of miRNA microarrays: human, mouse and rat. Each slide contains 8 identical arrays (8x15k) and each array contains over 15,000 60-mer oligonucleotides probes generated from recent versions of Sanger miRBase. Probes are representative of mature miRNA species and allow for increased sensitivity due to their hairpin design.

How much total RNA is required for labelling?

Depending on the platform, different amounts of total RNA are required. It is important that the extraction method does not exclude the small molecular weight RNA population. Please contact us for specifications and requirements.

Should I provide miRNA-enriched RNA, miRNA only, or total RNA?

The Agilent miRNA labelling protocol recommends total RNA; however, you must be certain to use an extraction method that does not eliminate the small RNA components. At this time miRNA enriched RNA and fractionated miRNA are not recommended.

Which extraction method is recommended?

Agilent recommends using Qiagen’s miRNeasy Mini Kit, Applied Biosystem miRVana™ RNA Isolation Kit, or Invitrogen’s TRIZOL® reagent. For the isolation kits, it is recommended that you follow the total RNA extraction protocols. With TRIZOL® reagent care must be taken that all residual TRIZOL® is removed from the extraction as any remaining will negatively effect the labelling reaction. Additional chloroform extractions can be performed in order to completely remove TRIZOL® from the extraction (this will slightly decrease the overall yield of the RNA).

What are the quality requirements for the RNA to be used for miRNA labelling?

Total RNA must have a 260/230 UV-Absorbance ratio greater than 1.8 and a RIN (Agilent Bioanalyzer) greater than 7.5. We will check sample quality using the Agilent Bioanalzyer total RNA Nano assay to ensure RNA is not degraded (which would result in a RIN less than 7.5). We will also check 260/230 ratio on the NanoDrop. Customers will have the option of continuing with their experiments if their samples do not pass QC; however, we will not guarantee the results under these conditions.

Are microRNAs selectively labelled?

Agilent’s miRNA Labelling Reagent and Hybridization kit uses a novel Cyanine 3-nucleotide [cyanine 3-Cytidine bisphosphate (pCp)] which selectively labels and hybridizes mature miRNAs. The Agilent platform is a 1-colour assay.

If I opt for the data analysis service, what data will I receive?

Please contact us for details regarding analysis.

What are the quality requirements on RNA to be used for miRNA labelling?

Total RNA must have a 260/230 UV-Absorbance ratio greater than 1.8 and a RIN greater than 7.5. We will check sample quality using the Agilent Bioanalzyer total RNA Nano assay to ensure RNA is not degraded (which would result in a RIN less than 7.5). We will also check 260/230 ratio on the Nanodrop. Customers will have the option of continuing with their experiments if their samples do not pass QC, however, we will not guarantee the results that will be obtained.