nCounter® miRNA Expression Panels

Accelerating Your Research with microRNA (miRNA) Profiling

A powerful tool for detecting small RNAs in challenging sample types and extracellular vesicles

Despite up to 30% of human genes being regulated by microRNA (miRNA), most conventional small RNA profiling technologies like miRNA sequencing can be costly, onerous, and require complex data analysis. In addition, they require RNA purification and multiple enzymatic steps that can be challenging for biofluid samples like serum and plasma. And when it comes to trying to detect miRNA in extracellular vesicles, the small strand length and low natural abundance volume makes that even more challenging.

When developing reliable and robust miRNA signatures for different diseases, you need a robust and reliable platform that works well with multiple sample types. 

nCounter miRNA Expression Panels utilize NanoString’s amplification-free technology to do expression profiling by direct quantification of individual RNA molecules. The assay detects miRNAs without the use of reverse transcription or amplification by using molecular barcodes.

Therefore, it is easier and faster to validate miRNA biomarkers compared to small RNA sequencing, GeneChip arrays, or TaqMan MicroRNA assays, and the results are highly reproducible. Additionally, since nearly all miRNA reads in the literature are associated with 200-300 miRNAs, it is best to work with a platform that maximizes the biologically relevant coverage, but delivers fast turnaround time when working in biomarker discovery.

With nCounter miRNA Expression Panels, you can:

  • Reliably detect and quantitate the most biologically relevant human or mouse miRNAs
  • Generate results directly from FFPE, blood, or biofluids
  • Utilize a chemistry that allows unambiguous discrimination of miRNAs with single nucleotide differences and six logs of dynamic range 
  • Streamline workflows with cost effective panels that take <1 hour hands-on time and get publication ready results within 24 hours
  • Access protocols for detecting miRNA in extracellular vesicles
MicroRNA (miRNA) appears in many different sample types, but is challenging to detect, especially in extracellular vesicles. NanoString has off the shelf panels that detect high confidence and clinically-relevant miRBASE miRNAs for mouse and human.

How It Works

The nCounter miRNA Expression Panels are a unique collection of the most biologically and clinically relevant mature miRNA molecules according to the most recent miRBase database release. It covers 827 human and 577 mouse microRNAs. The panel is designed to provide a sensitive, reproducible, and highly multiplexed method for detecting miRNAs in total RNA across all biological levels of expression. The assay can be run on total RNA isolated from any source, including formalin-fixed paraffin embedded (FFPE) tissue sections, but also blood and biofluids. Many researchers have also used it to measure miRNA expression levels in extracellular vesicles in tissue. 


Off-the-shelf assays are available for probing hundreds of human and mouse miRNAs


Create a custom a la carte miRNA assay

Pick 20-50 miRNAs of your choice from the list of miRNAs included in the human and mouse miRNA panels


Custom design options

Hot miRNA Research Areas

The nCounter Human v3 miRNA Panel covers all the high confidence miRNAs identified by miRBase

miRNA-mRNA Interactions

One of the most common miRNA research areas involves interrogating miRNA-miRNA interactions. Since microRNAs are key regulatory molecules that function by binding directly to mRNA, they can cause less efficient translation of the target mRNAs. MiRNA-mRNA interactions are important for the following application areas:

Exosomes and Extracellular Vesicles

Despite their discovery more than 35 years ago, knowledge of exosomes (and extracellular vesicles) and the role they play in disease is an emerging area of research. They are found in multiple types of extracellular fluids, such as blood and biofluids. The challenge, however, is to identify, isolate, and quantify exosomes accurately, efficiently, and most importantly, selectively.

Check out our white paper on applications with exosomes and extracellular vesicles in miRNA research.

How the microRNA (miRNA) Expression Panel was Developed

High miRBase Coverage

In bioinformatics, the miRBase database is considered the best source of information on microRNA sequences and annotation.

Although there are more than 38,000 known miRNA sequences, only a fraction of those are considered biologically relevant or useful for potential clinical applications. A confidence level has been assigned to each miRNA hairpin based on a set of quantitative guidelines associated with the mapping of sequencing reads.

The nCounter miRNA panels contain a probe for all the miRNA hairpins denoted as “high confidence”. Additionally, NanoString uses proprietary metrics such as observed read ratios and expression analytics in order to screen potential content for inclusion in the panel. Together, these methods help ensure that the miRNA panel content is heavily weighted toward biologically significant miRNAs, making it ideal for biomarker discovery and validation.

Panel Selection Tool

Find the gene expression panel for your research with easy to use panel pro

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Related Resources

View All Resources
Product Bulletin miRNA – Product Bulletin
Whitepaper Human miRNA – Whitepaper
App Note/Tech Note Tech Note – miRNA Analysis in Plasma and Serum
Blog Post miRNA Profiling in Malignant Melanoma: Making “Australia’s National Cancer” Obsolete.

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