Analyzing the expression of miRNAs in qbase+

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microRNAs (miRNAs) are small non-coding (not translated into proteins) RNAs that regulate gene expression. They bind to complementary sequences in mRNA. As a result, these mRNAs can no longer be translated into proteins and miRNA-mRNA complexes are targeted for breakdown.

miRNAs are produced by transcription[1], so their production can be measured by qPCR and analyzed in qbase+ in the same way as the production of mRNA is.

The experiment consists of a single run: Run12
The expression of the following miRNAs was measured:

  • 2 reference targets: miRNAs RNU24 and RNU48
  • 2 targets of interest: miRNAs mir-92 and mir-628

There are two technical replicates per reaction.

Sample annotation can be found in a separate sample properties file.

Creating a new experiment

Loading the data

To analyze and visualize the analysis results in a later stage, we are going to add a custom sample property: MYCN status.

MYCN is a transcription factor. Amplification and overexpression of MYCN is known to lead to tumorigenesis. The experiment that we are analyzing tries to assess whether the expression of the two target miRNAs of interest is related to the copy number of MYCN.

Analyzing the data

We have done previous qPCR experiments with these primer pairs and we known from these previous experiments that

  • amplification efficiencies for the reference targets are 95%
  • amplification efficiencies for the targets of interest are 98%

Look at the target bar charts.