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The nCounterâ„¢ Analysis System measures transcript abundance by tagging and counting individual mRNA molecules using a novel fluorescent barcoding technology. The system is able to detect 1 copy of mRNA per cell, can measure up to 800 genes per reaction, and requires only 10-100 ng of total RNA for analysis. The nCounter can also be used for miRNA profiling and CNV analysis.


  • Fills the throughput niche between qPCR and microarrays for "mid-multiplex" assays
  • Ideal for assays of dozens to hundreds of genes in 50+ samples
  • More time-efficient and cost-effective than qPCR
  • Direct measurement of transcript abundance (No amplification, digital readout)


Sample Submission/Preparation

New users should contact WIGTC for training and consultation. Custom CodeSets* are designed by Nanostring specifically for your assay. CodeSet pricing varies with number of targets and samples. Delivery times for CodeSet design and synthesis can be several weeks.

Typically 100 ng of total RNA is recommended though the assay is very tolerant to smaller inputs or partially degraded samples such as from FFPE.

(*A CodeSet is the collection of reporter and capture probes for all genes of interest in the assay).


How do you normalize the data?

First normalize using the internal system controls to remove any slight assay-to-assay system variation and then normalize using 3-4 validated endogenous controls.

Can I compare the nCounter System with my microarray data?

Yes. The fold change data obtained from an nCounter analysis should correlate with fold change results obtained from microarray analyses.

Can nCounter data be used together with qPCR data?

Yes, both in terms of relative expression levels and fold changes.

How do I analyze my data?

The comma separated value file returned by the nCounter system is easily imported and analyzed in other programs, including Excel.

Is there documentation available about analyzing my data?

Yes, there is a data analysis guidelines document that is available in the Product Literature from Nanostring. You can download it here:


Please refer to the Pricing Section

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