- NanoString technology is a highly sensitive and multiplexed platform for the direct quantification of nucleic acids, particularly messenger RNA (mRNA), without the need for reverse transcription or amplification. This makes it an attractive option for gene expression analysis, especially when working with limited, degraded, or complex biological samples such as formalin-fixed paraffin-embedded (FFPE) tissues.
- At the core of NanoString’s gene expression platform is the nCounter® Analysis System, which employs molecular barcoding and digital detection to measure the expression levels of up to 800 genes simultaneously in a single reaction. Each target gene is detected using a pair of sequence-specific probes: a capture probe and a reporter probe. The reporter probe carries a fluorescent barcode unique to each target, while the capture probe enables immobilization of the target-probe complex during data collection.
- After hybridization of probes to target RNA molecules (typically 12–24 hours at 65°C), the tripartite complex (target RNA + reporter + capture probe) is purified and immobilized on a cartridge. The sample is then scanned by the nCounter Digital Analyzer, which counts the fluorescent barcodes directly, providing absolute quantification of each transcript without enzymatic steps that can introduce bias.
- NanoString gene expression assays are widely used in basic research, translational studies, and clinical applications. The platform is especially valued for its robustness, reproducibility, and compatibility with challenging sample types. It has been used extensively in oncology, immunology, neuroscience, and infectious disease research. Additionally, NanoString offers pre-designed gene panels (e.g., PanCancer Pathways, Immunology, Neuropathology) and customizable CodeSets, allowing researchers to tailor assays to specific biological pathways or disease contexts.
- Because NanoString provides digital counts rather than relative quantification, the data are straightforward to interpret and highly reproducible across different runs and laboratories. Moreover, the platform supports downstream analysis through NanoString’s nSolver™ Analysis Software, which offers normalization, statistical testing, and data visualization tools.
- In summary, NanoString technology represents a reliable and efficient alternative to qPCR and RNA sequencing for gene expression profiling, particularly when working with low-input or degraded RNA, and when a targeted, multiplexed approach is required.
