nCounter Applications and Solutions

NanoString technology uses unique color-coded molecular barcodes that can hybridize directly to many different types of target nucleic acid molecules, making it ideal for a range of discovery and translational research applications. Our portfolio of application-specific solutions currently includes kits for gene expression, copy number variation and miRNA analysis.

We are committed to expanding the range of applications enabled on the nCounter Analysis System and are continually working with customers and other partners to develop novel solutions for current and emerging areas of biological research and discovery.




Add hybridization buffer, the target-specific CodeSet, and biological sample to a single tube. Hybridize overnight.


Inject hybridized samples into an nCounter Cartridge.


Insert the cartridge, select run, and press “Start Processing.”


Download raw data directly from the nCounter SPRINT Profiler to a USB flash drive or your networked computer.

Gene Expression Analysis

Gene Expression CodeSets for the nCounter Analysis System offer a cost-effective way to analyze the expression levels of up to 800 genes simultaneously, with sensitivity comparable to qPCR. The system can directly assay tissue and blood lysates as well as FFPE extracts in a simple workflow that only requires 15 minutes of hands-on time per reaction.

Gene Expression Analysis

Single Cell Gene Expression Analysis

The nCounter Single Cell Gene Expression Assay provides a superior approach to identifying cell-to-cell differences within a population of cells. It is a highly multiplexed, single tube assay that allows the analysis of 20 – 800 genes and frees you from the constraints of fixed format microfluidic platforms.

Single Cell Expression Analysis

miRNA Expression Analysis

With multiplexed target profiling of miRNA transcriptomes in a single reaction, the nCounter miRNA Expression Assay Kits deliver high levels of sensitivity, specificity, precision, and linearity across a wide range of research areas such as oncology, neurobiology, developmental biology, and stem-cell research.

miRNA Expression Analysis

miRGE™ Analysis

Revolutionizing the workflow for profiling miRNA and mRNAs expression, nCounter miRGE CodeSets allow for the simultaneous profiling of both miRNAs and mRNAs in a single reaction. Two assays in a single tube means fewer pipetting steps, less preparation time and only a single sample aliquot. miRGE CodeSets can profile samples from FFPE extracts, as well as from several other precious/difficult sample types.

miRGE Analysis

Copy Number Variation Analysis

The nCounter Copy Number Variation CodeSets enable better results, faster, and with substantially less effort than PCR or arrays. With the lowest hands-on time of any platform, these CodeSets provide everything needed to interrogate copy number variants in a single multiplexed reaction.

Copy Number Variation Analysis

lncRNA Expression Analysis

The nCounter Custom lncRNA Assay enables researchers to study focused sets of up to 800 lncRNAs with high precision and less hands-on time than any other platform. These assays are ideal for high-precision studies of lncRNAs across large sample sets or involving many experimental conditions. lncRNAs and mRNAs can be combined in a single codeset.

lncRNA Expression Analysis

ChIP-String Expression Analysis

The nCounter Custom ChIP-String Assay is a read-out method designed to measure dsDNA fragments that have been enriched via various user-defined chromatin immunoprecipitation protocols. Based on NanoString’s molecular barcoding technology the assay can reliably quantify as few as 5,000 molecules of DNA without the need for amplification.

ChIP Expression Analysis

Leukemia Fusion Gene Analysis

The NanoString nCounter Leukemia Fusion Gene Expression Assay Kit allows researchers to 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.

Leukemia Fusion Gene Analysis

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