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affymetrix: miRNA
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The UHNMAC now offers the Affymetrix platform for micro-RNA (miRNA) profiling. The GeneChip® miRNA Array is based on Version 15 of the Sanger miRBase and includes miRNA sequences from 131 organisms (including human, mouse, rat, canine, monkey, etc.) on a single array. The GeneChip miRNA 2.0 Array also includes human small nucleolar RNAs (snoRNAs and scaRNAs), which are short, non-translated RNAs that play a role in processing of ribosomal RNAs following transcription. snoRNAs have also been implicated in the regulation of alternative splicing.



The GeneChip miRNA 2.0 Array includes:
  • 15,644 probe sets in total (100% miRBase v15 coverage
  • 2,202 human, mouse and rat hairpin pre-miRNAs
  • 2,334 snoRNA and scaRNA probes
  • 107 retrospective miRNA, scaRNA and snoRNA probe sets from previous-generation array
For more information, please visit the Affymetrix miRNA website.

Service includes (1-Colour):
  • Total RNA Quality Checked with Agilent BioAnalyzer ($10 fee is charged if RNA quality deemed too low quality to proceed with the experiment)
  • Labelling of one RNA sample per array using FlashTag™ Biotin RNA Labeling kit (Genisphere)
  • Hybridisation/washing/scanning of arrays
  • Generation of .dat, .cel, .chp and rpt files
  • Output files sent to customer (via Data Portal)
We also offer an optional data analysis service.

Sample Requirement:

High quality total RNA is required for microarray experiments. The FlashTag™ Biotin labelling system is a one colour system and each labelling reaction requires 200 ng of total RNA. Extraction kits often result in the best RNA quality for this labelling protocol as they are able to more completely eliminate residual organics (such as phenols) during purification; hence, improving subsequent labelling efficiency. The 260/230 absorbance ratio is a good indicator of organic contamination and RNA of a 260/230 ratio of greater than 1.8 is required in order to proceed with the miRNA array experiment. If using Trizol for RNA extraction, additional chloroform extractions are recommended to ensure all Trizol is removed. (Please note that each additional chloroform extraction may decrease the overall RNA yield but should increase its quality). The quality of the samples is checked upon arrival using the Agilent 2100 Bioanalyzer. An RNA Integrity Number (RIN) of 7.5 usually yields good results.

We request an additional 5 µL of total RNA (at a concentration of 100 ng/µL) to check the integrity of the RNA sample. If you have less than 5 µL available, please contact us to discuss your options. Please note that if samples do not meet quality control and the customer opts not to continue with the project, a fee of $15/sample will be charged.

Array Types and Format:

Affymetrix's comprehensive miRNA GeneChip is available in the mini-array (400) format. This array covers 71 different organisms and is based on version 11 of the Sanger miRBase database..

Pricing: Download (Last updated: September 2011)
Please note that this pricing is for academic groups. Commercial customers should contact us for a quote.

Contact: Affymetrix Service at

miRNA profiling is also available on the Agilent and NanoString array platforms.