NanoString nCounter Analysis
The nCounter® technology is a versatile platform well-suited for discovery and translational research. It supports a wide range of applications, including gene expression profiling, tumor profiling, immuno-oncology profiling, single-cell gene expression, miRNA analysis, gene fusion and copy number variation (CNV) analysis, lncRNA expression, and ChIP-String expression analysis.
This system enables the simultaneous digital detection of RNA, DNA, and protein within a single experiment, offering maximum flexibility for each project. By minimizing experimental variability, nCounter assays streamline sample analysis, delivering precise and reproducible measurements of gene expression for rapid target identification.
Cost-effective automation for multiplex analysis of up to 800 targets.
High precision and reproducibility in gene expression measurements (miRNA, RNA, CNV).
Extensive target panel options, including expertly curated panels with up to 770 genes, plus customization with an additional 55 unique targets.
Flexible panel design, allowing further customization with extra targets.
No amplification or library prep required — eliminates cDNA conversion, technical replicates, and complex workflows.
Fully digital target counting with direct quantitative output.
Streamlined sample preparation: assays can be performed directly on cell lysates or tissue homogenates, with optional RNA purification.
Simplified workflow automation, minimizing steps to improve reliability.
Fast turnaround — efficient data analysis with results available in less than 24 hours.
Service Features
Our services feature an extensive library of expertly curated gene expression panels, covering more than 20,000 genes that can be combined to create pathway- and disease-focused panels. Custom probe design is also available for any sequence of interest. With a commitment to efficiency, we ensure timely data delivery within two weeks or sooner. Backed by over 20 years of accumulated experience, our team offers expert data analysis and interpretation, along with reliable scientific and technical support.
Sample Requirements: Broad Compatibility
The nCounter® platform is compatible with a wide range of sample types, including total RNA, FFPE, cell lysates, PBMCs, plasma, serum, and even decades-old FFPE specimens. It requires only minimal input material— as little as 25 ng or 5,000 cells—making it well-suited for limited or precious samples. Primer pools are available for multi-target enrichment in cases of low input, ensuring flexibility and robust performance. The system enables the generation of high-quality data from samples that would otherwise be difficult to analyze with traditional high-input methods. Moreover, consistent and reliable results can be achieved for longitudinal studies, even when working with degraded, clinical-grade samples.
PlexSet™ Technology
For projects that require targeted, mid-plex analysis, PlexSet™ offers a flexible and cost-effective extension of the nCounter® platform. PlexSet enables researchers to design custom panels focused on specific genes of interest, providing the same high-quality digital detection and reproducibility as standard nCounter assays, but at a fraction of the cost.
With PlexSet, you can profile dozens to a few hundred genes in a single run, making it an ideal solution for biomarker validation, pathway-focused studies, and translational research that does not require the full scope of large fixed panels. Importantly, PlexSet assays run seamlessly on the nCounter Analysis System, ensuring compatibility with existing workflows and data analysis pipelines.
By combining affordability with the proven accuracy of nCounter technology, PlexSet empowers researchers to generate actionable insights without compromise.
Fields of Application
Gene Expression Profiling
Transcriptome analysis is a powerful approach for exploratory studies such as drug target discovery and biomarker identification in specific diseases. Because of its responsiveness to both external and internal stimuli, the transcriptome provides valuable insight into disease prediction and progression.
NanoString technology enables enzyme-free, cDNA conversion- and amplification-free gene expression analysis, requiring as little as 25 ng of input material. It is compatible with a wide variety of sample types, including total RNA, plasma, serum, PBMCs, FFPE, and cell lysates. With panels ranging from 200 to 770 genes, researchers can access curated content across diverse fields such as immunology, oncology, and neurology. Panels are available for both human and mouse models, offering broad applicability.
With a strong track record, NanoString has delivered state-of-the-art solutions for RNA expression analysis across multiple disease areas. Its comprehensive panel offerings include gene expression signatures with demonstrated clinical utility in immuno-oncology, breast cancer, lymphoma, and related fields.
Learn more about Established and Clinically Relevant Gene Expression Profiling Signatures.
miRNA Expression Profiling
NanoString® miRNA Expression Panels have been developed for profiling human, mouse, and rat miRNAs. These panels utilize specific oligos to enhance the detection of small ~22 nucleotide miRNAs. The assays incorporate a target-specific bridge oligo and miRTag, in addition to capture and reporter probes, which extend the miRNA length for improved hybridization. The extended miRNA–miRTag complex is then detected and quantified using standard nCounter® chemistry.
The human, mouse, and rat panels contain 827, 577, and 423 assays, respectively. Approximately 100 ng of total RNA is required for analysis. Learn more about these panels.
With nCounter® miRNA Expression Panels, researchers can:
Reliably detect and quantify biologically relevant human or mouse miRNAs.
Generate results directly from FFPE, blood, or biofluid samples.
Apply robust chemistry that distinguishes miRNAs with single nucleotide differences and up to six logs of dynamic range.
Streamline workflows with cost-effective panels requiring <1 hour of hands-on time and producing results within 24 hours.
Access protocols optimized for detecting miRNA in extracellular vesicles.
CNV & Gene Fusion
Copy number variations (CNVs) are implicated in a wide range of diseases, from genetic disorders to cancer. While FISH has traditionally been used to detect CNVs, the increasing importance of these variations has made higher-plex technologies such as microarrays and next-generation sequencing (NGS) more attractive. However, these approaches can be time-consuming, cumbersome, and often require specialized expertise. Moreover, most microarrays are not well-suited for detecting CNVs from FFPE samples.
NanoString® provides dedicated assays for Copy Number Variation (CNV) analysis and Gene Fusion analysis, both optimized for FFPE tissue samples. PicolImmune simplifies this process with NanoString’s CNV and Gene Fusion panels, ensuring reliable and efficient data generation.
CNVs occur when a section of the genome is repeated, and the number of repeats varies across a population. Such variations can disrupt normal protein function, potentially leading to disease. NanoString’s Human Cancer CNV panel enables detection of 87 genes commonly amplified or deleted in cancer. Analysis requires only 300 ng of genomic DNA.
Gene fusions, by contrast, involve the joining of two separate genes due to chromosomal rearrangements, resulting in a hybrid gene. These events are often key drivers in cancer, with the fusion product acting as an oncogene. The Gene Fusion Assay requires approximately 100 ng of total RNA, or up to 300 ng if derived from FFPE tissue.
Resources
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