UNIT 25B.10 Digital Multiplexed Gene Expression Analysis Using the NanoString nCounter System

  1. Meghana M. Kulkarni

Published Online: 1 APR 2011

DOI: 10.1002/0471142727.mb25b10s94

Current Protocols in Molecular Biology

Current Protocols in Molecular Biology

How to Cite

Kulkarni, M. M. 2011. Digital Multiplexed Gene Expression Analysis Using the NanoString nCounter System. Current Protocols in Molecular Biology. 94:B:25B.10:25B.10.1–25B.10.17.

Author Information

  1. Harvard Medical School, Boston, Massachusetts

Publication History

  1. Published Online: 1 APR 2011
  2. Published Print: APR 2011


This unit presents the protocol for the NanoString nCounter Gene Expression Assay, a robust and highly reproducible method for detecting the expression of up to 800 genes in a single reaction with high sensitivity and linearity across a broad range of expression levels. The methodology serves to bridge the gap between genome-wide (microarrays) and targeted (real-time quantitative PCR) expression profiling. The nCounter assay is based on direct digital detection of mRNA molecules of interest using target-specific, color-coded probe pairs. It does not require the conversion of mRNA to cDNA by reverse transcription or the amplification of the resulting cDNA by PCR. Each target gene of interest is detected using a pair of reporter and capture probes carrying 35- to 50-base target-specific sequences. In addition, each reporter probe carries a unique color code at the 5′ end that enables the molecular barcoding of the genes of interest, while the capture probes all carry a biotin label at the 3′ end that provides a molecular handle for attachment of target genes to facilitate downstream digital detection. After solution-phase hybridization between target mRNA and reporter-capture probe pairs, excess probes are removed and the probe/target complexes are aligned and immobilized in the nCounter cartridge, which is then placed in a digital analyzer for image acquisition and data processing. Hundreds of thousands of color codes designating mRNA targets of interest are directly imaged on the surface of the cartridge. The expression level of a gene is measured by counting the number of times the color-coded barcode for that gene is detected, and the barcode counts are then tabulated. Curr. Protoc. Mol. Biol. 94:25B.10.1-25B.10.17. © 2011 by John Wiley & Sons, Inc.


  • gene expression signature;
  • multiplex analysis;
  • signal transduction;
  • high-throughput screening;
  • molecular barcode