BLOG: Choosing the Right RNA Analysis Method: RNA-Seq, NanoString, or qPCR?

When studying gene expression, researchers commonly turn to one of three main technologies: RNA sequencing (RNA-Seq), NanoString nCounter®, or quantitative PCR (qPCR). Each method offers unique benefits and trade-offs depending on the research goal, sample type, budget, and timeline.

RNA Sequencing (RNA-Seq): From Discovery to Focused Applications

RNA-Seq is a powerful and flexible approach that uses next-generation sequencing (NGS) to quantify RNA molecules. It comes in two primary formats:

- Transcriptome-wide RNA-Seq sequences all RNA transcripts in a sample, offering an unbiased, comprehensive view of gene expression. It enables the discovery of novel transcripts, splice variants, non-coding RNAs, and gene fusions. With its high sensitivity and dynamic range, it is ideal for exploratory research and biomarker discovery. However, this approach requires high-quality RNA, deep sequencing coverage, and sophisticated bioinformatics support. It is also resource-intensive in terms of cost and computational demands.

- Targeted RNA-Seq panels take a focused approach by sequencing a predefined set of genes associated with particular pathways, disease signatures, or therapeutic relevance. These panels use either amplicon-based PCR or hybrid-capture methods to enrich for selected transcripts, followed by NGS. Targeted panels offer high-depth coverage of specific genes, enabling the detection of low-abundance transcripts, isoforms, and gene fusions at a lower cost than transcriptome-wide RNA-Seq. However, their scope is limited to the selected targets and they are not suitable for novel transcript discovery.

NanoString nCounter®: Direct Detection for Challenging Samples

The NanoString nCounter® system uses digital molecular barcodes to directly count mRNA molecules—without the need for reverse transcription or PCR amplification. This minimizes bias and preserves the original abundance of transcripts, making it particularly effective for working with degraded or FFPE-preserved RNA samples. Its simple hybridization-based workflow can deliver results in under 48 hours and requires minimal bioinformatics support.

However, NanoString panels are limited to around 800 genes per run and cannot detect novel transcripts or structural variants. Its dynamic range is also narrower than RNA-Seq, reducing sensitivity for very low-expressing genes. Despite these limitations, NanoString is an excellent choice for validation studies, clinical research, and regulatory submissions where robustness and speed are key.

qPCR: Precision for Small-Scale Expression Analysis

Quantitative PCR (qPCR) remains a gold standard for gene expression analysis when only a few genes are being studied. It is fast, affordable, and highly sensitive, making it ideal for validating RNA-Seq or NanoString results. qPCR assays typically target 1–10 genes at a time and can be completed in 1–3 days using minimal RNA input.

However, qPCR lacks the scalability and multiplexing capabilities of RNA-Seq or NanoString, and it requires prior knowledge of target genes. It is not suitable for transcript discovery, and amplification steps can introduce bias at extreme input levels. Nonetheless, for small, hypothesis-driven studies or clinical validation of known biomarkers, qPCR is unmatched in efficiency and precision

Conclusion

No single RNA analysis method fits every research need. RNA-Seq excels in discovery and scalability, NanoString offers robustness and simplicity for fixed panels, and qPCR provides speed and precision for low-plex validation. By aligning the method with the biological question, sample constraints, and available resources, researchers can maximize the impact and accuracy of their gene expression studies.

To learn more how our scientific team can support your RNA Analysis, contact Eurofins Clinical Trial Solutions or explore our technologies.