nCounter® Custom CodeSets

A Custom CodeSet is a multiplex assay of up to 800 user-defined targets. Our bioinformatics team has worked with customers to design CodeSets for a variety of organisms and applications, incuding: Gene Expression, Copy Number Variation (CNV), Fusion or Splice Variant detection, Ribosomal RNA, and more.

Our web-based tool, nDesign™ Gateway, allows you to explore gene content and design your own CodeSet for human, mouse, or rat genes. For more complex designs or for other organisms, contact us today to discuss your design with our bioinformatics team.

  • CodeSets designed to your specifications
  • Include up to 800 targets of interest
  • Designs to any organism with known sequence
  • Expert bioinformatics design support

nCounter Custom CodeSet Design Process

nCounter Custom CodeSet design process

Expand Your CodeSet with CodeSet-Plus 

Custom CodeSets can be updated over time with up to 30 additional targets with CodeSet Plus, a small custom CodeSet that can be spiked into larger, previously ordered CodeSets.


Product Description Catalog Number NAV Number Unit Size
nCounter mRNA Custom CodeSet Custom CodeSet for detection and quantification of mRNA Transcripts (including Fusion Genes and Splice Variants) Varies by product configuration Varies by product configuration Per probe
nCounter CNV Custom CodeSet Custom CodeSet for Copy Number Variation analysis Varies by product configuration Varies by product configuration Per probe
nCounter ChIP-String Custom CodeSet Custom CodeSet for analysis DNA prepared by Chromatin Immunoprecipitation (ChIP) Varies by product configuration Varies by product configuration Per probe
nCounter CodeSet Plus Custom CodeSet containing up to 30 probes that can be spike-in into another Custom CodeSet. Varies by product configuration Varies by product configuration Per probe
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For Research Use Only. Not for use in diagnostic procedures.