NanoString nCounter


nCounter® Analysis System from Nanostring Technologies is a medium-high throughput gene expression quantification system that is based on direct multiplexed measurement of gene expression.


  • Expression Analysis
    • Pre-built panels: off-the-shelf preassembled CodeSets, ready to be run.
    • Virtual panels: Select your CodeSet from lists of genes representing  specific genetic pathways, disease states and biological processes.
    • Custom CodeSets: Have your own CodeSet designed by providing a list of your targets.
      • mRNA: select up to 800 target transcripts to be analysed in one multiplexed reaction.
      • lncRNA: select up to 800 lncRNAs for analysis in a single multiplexed reaction.
      • À la carte miRNA: analysis of subsets of miRNAs included in species-specific miRNA Expression Assay Kits.
    • miRNA Expression (Human, Mouse, Rat, and Drosophila)
    • miRGE: miRNA and mRNA expression analysis in one single assay. A number of 5-30 miRNA and 100-200 mRNA molecules can be selected for analysis
  • CNV Analysis (more info here)

    • CNV Custom CodeSet: Investigate up to 800 different putative CNV regions
    • v2 Cancer CN Assay: copy number quantification for 87 genes commonly amplified or deleted in cancer
    • Human Human Karyotype Panel: simultaneous measurement of all 24 human chromosomes, including 338 individual loci
  • Leukemia Fusion Gene Expression Assay Kit:  profile a comprehensive set of fusion genes which result from balanced translocations in different leukemia sub-types. In addition to leukemia fusion genes, the kit includes probes for 11 wild-type genes involved in the different translocations, 12 leukemia-related biomarkers, and 2 normalization genes. More info here.


Basic Bioinformatics Analysis

For each experiment, we perform a data quality control of which you will receive a detailed report in PDF format. This report contains a description of the experiment (which samples have been run on which position of the cartridge), analysis of positive and negative controls, and scaling factors, and correlation heatmaps. We will also normalize the data according to the Nanostring Data Analysis Guidelines using a scaling approach against the positive controls.

More detailed bioinformatics analysis can be performed within VIB Nucleomics Core bioinformatics service.



Next to the raw data, you will receive a detailed quality control report and an Excel or tab-delimited text file containing the normalized data (but also the data of each intermediate step during data pre-processing) for each sample.

Sample submission