GeneChip™ miRNA 3.0 Array - FAQs

The species information can be found in the annotation file of the miRNA array of interest.
Please complete the following steps:
- Go to www.thermofisher.com and go to the product page of the array of interest.
- Scroll down to support files.
- Download the annotation files for the miRNA array of interest, and open in excel.
- In the file, there will be a column, species scientific name. This column will have all the species present on the array.

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The ERCC controls are not tiled onto GeneChip miRNA arrays because they would not work with the miRNA array/assay system. The FlashTag Biotin HSR RNA Labeling Kits used to label miRNAs is optimized for shortRNAs. Even though longer mRNAs like the ERCC controls will be labeled, the HWS (hyb/wash/stain) conditions are not optimal and consequently, the longer mRNAs typically do not get detected.

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Due to certain miRNAs being conserved across species, there may be multiple copies of the same probe across the miRNA arrays. However, sample processing with the FlashTag Biotin HSR RNA Labeling Kits ensures that there is excess target compared to the probes on the array. Consequently, there is enough sample available to hybridize onto all the replicate probes.

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The miRNA interaction network in TAC Software is available for all gene arrays, including model organisms. To have the interaction network available, the same samples must have been processed through both the gene array and the miRNA array. Additionally, the gene array being used must have a gene symbol column displayed in their annotation.

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GeneChip miRNA 3.1 Array Strips provide a linear dynamic range (> 3 log10) that is similar to that provided by the GeneChip miRNA 3.0 Array cartridges. When evaluating non-control probe sets that are common to both arrays, we observed very high signal correlation (Pearson correlation coefficients of 0.97 - 0.98 for signal correlation) and fold change value correlation (Pearson correlation coefficients of 0.95 - 0.97 for fold change value correlation) for GeneChip miRNA 3.0 Array cartridges compared to GeneChip miRNA 3.1 Array Strip.

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For the miRNA 3.0 array data, we used 16 spiked miRNA transcripts and measured linearity of median spike signal over a broad range of concentration, similar to the platform comparison document. So Fig. 3 in the tech note, linked here: http://media.affymetrix.com/support/technical/technotes/mirna2_array_technote.pdf, shows the signal with spikes at 0.1, 1, 10 and 100 attomoles/100 ng.

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