Institute of Human… Research Neurogastrogenetics … nCounter Core…

The nCounter Core Facility

The nCounter Core Facility has been established to provide access to one of the current state of the art expression profiling technologies for the Heidelberg University research community. It is supported by the Excellence Cluster Cell Networks and the DFG.

The nCounter System

The nCounter system from Nanostring Technologies is a complete, fully automated system for the next generation of digital gene expression analysis.

The nCounter system is an instrument designed for multiplexed measurement of gene expression using fluorescently labeled reporter probes, so called ‘codesets’. The codeset probes are ca 100 bases in length. Therefore, the system is very resistant to lower RNA quality and is perfectly suited for critical samples such as FFPE (formalin-fixed, paraffin-embedded) samples.
Applying a unique coding technology enables direct counting of individual RNA molecules across all levels of biological expression, with sensitivity and specificity comparable to Real Time PCR (RT PCR). The main advantage is that no enzymatic reactions are involved, in particular no reverse transcription is necessary.

In addition, it is suitable for analysis of as little as 600 ng of genomic DNA (karyotyping and copy number variation (CNV) analysis).


  • Low amount of input material (100 ng of total RNA⁄sample) / 600 ng DNA
  • Ability to analyze RNA samples of poor quality (such a FFPE samples)
  • Up to 800 transcripts can be simultaneously interrogated per sample
  • No enzymatic reactions involved
  • Very high dynamic range, sensitivity and reproducibility
  • Perfect tool for microarray validation, pathway analysis, expression analyses of defined gene sets and for biomarker validation


  • mRNA Profiling
    custom set of genes or off-the-shelf preassembled panels
  • miRNA Profiling
    comprehensive collection of more than 700 human and human-associated viral miRNAs as well as murine miRNAs derived from miRBase
  • Analysis of DNA (CNVs and karyotypes)

Codeset ordering information can be found on the NanoString website. For ordering, please contact nanostring directly via Email.

Further reading: The technology has first been described by Geiss et al., 2008. Direct multiplexed measurement of gene expression with color-coded probe pairs. Nature Biotechnology 26, 317-325.