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LncRNA qPCR assays for accurate and reliable RNA expression analysis

LncRNA qPCR assays are essential tools for accurate quantification of long non-coding RNA expression, a critical step in gene expression studies and RNA-seq validation.

However, lncRNA analysis is technically challenging due to low expression levels, transcript complexity, and specificity issues.

Developed and experimentally validated by AnyGenes, a biotechnology company specialized in gene expression analysis and qPCR solutions, with a dedicated R&D team based in France and extensive experience in complex RNA analysis, these assays are designed to deliver reliable and reproducible results, even for complex lncRNA targets.

In addition to qPCR assays, AnyGenes provides gene expression analysis and RNA-seq validation services, supporting researchers worldwide.

Robust lncRNA expression profiling with AnyGenes® qPCR arrays

Why are lncRNA qPCR assays challenging to design and use?

LncRNAs present unique analytical difficulties compared to protein-coding genes:

  • Low abundance, requiring high sensitivity detection
  • Multiple transcript isoforms, increasing the risk of non-specific amplification
  • Genomic overlap with coding genes
  • Background noise affecting qPCR accuracy
  • Variable annotation across databases

These challenges often result in poor reproducibility and unreliable quantification when using non-validated primers.

Reliable quantification requires careful primer design and experimental validation.

How to analyze low-expression lncRNAs with qPCR using SpeAmp®?

Low-expression lncRNAs can be difficult to detect with standard qPCR workflows, especially when working with limited RNA input, FFPE samples, or single-cell material.

To improve detection sensitivity, cDNA preamplification can be applied prior to qPCR analysis. This strategy is particularly useful for lncRNA studies, where weak signals can limit accurate quantification.

The SpeAmp® qPCR preamplification system, developed by AnyGenes, is designed to enable reliable detection of low-abundance RNA targets while maintaining reproducible results.

This approach helps researchers:

  • strengthen qPCR signal detection
  • improve analysis of low-input samples
  • support RNA-seq validation experiments
  • generate more consistent expression data

Validated lncRNA qPCR assays for reliable results

These kits are designed to ensure high performance and reliability across a wide range of experimental conditions, including challenging samples.

They are developed with several key characteristics that support accurate and reproducible gene expression analysis:

  • All-in-one, ready-to-use format for simplified workflows
  • Optimized primer design targeting exon-exon junctions whenever possible
  • Reduced risk of genomic DNA amplification
  • Compatibility with low-quality or limited RNA samples (FFPE, LCM)
  • Optimized performance with Perfect Master Mix SYBR® Green

Together, these features enable accurate detection and quantification of low-expressed and structurally complex lncRNAs.

From RNA-seq to qPCR: why lncRNA qPCR assays are essential

RNA sequencing is widely used to identify lncRNA candidates, but these assays remain essential for validation. Key reasons:
  • RNA-seq may produce false positives
  • Low-abundance transcripts require higher sensitivity
  • qPCR provides quantitative confirmation of expression levels
Using validated assays enables:
  • Reliable RNA-seq validation
  • Accurate fold change measurement
  • Confirmation of biomarker candidates
RNA-seq results require validation due to variability and sensitivity limitations, as described in MIQE guidelines (Bustin et al., 2009).

LncRNA qPCR assays formats: primers and arrays

These kits are available in flexible formats to suit different experimental needs:

Individual primer sets

  • Validated assays for specific targets
  • Ideal for focused validation studies

96- and 384-well qPCR arrays

  • Ready-to-use panels
  • Suitable for multi-target screening and pathway analysis

Custom qPCR panels

  • Designed based on your gene list

Adapted to your biological model and research objectives

How to choose the right lncRNA qPCR assays?

Selecting appropriate lncRNA qPCR assays depends on:

  • Target complexity (isoforms, overlapping transcripts)
  • Expression level
  • Number of genes to analyze
  • Experimental workflow (screening vs validation)

Validated assays ensure specificity, reproducibility, and reliable quantification, especially for challenging lncRNA targets.

International availability

AnyGenes products and services are available worldwide through a network of international distributors, supporting researchers across Europe, Asia, and North America.

Applications of lncRNA qPCR assays

These qPCR solutions  are widely used in:

  • Cancer research: identification of diagnostic and prognostic biomarkers
  • Immunology: regulation of immune signaling pathways
  • Cardiovascular diseases
  • Neuroscience research

They are particularly valuable for:

  • Biomarker discovery
  • Gene expression profiling
  • Signaling pathway analysis

Expert insight

LncRNA qPCR analysis often fails due to poor specificity and low signal detection.

For complex targets, experimentally validated assays are essential to ensure reproducibility and reliable quantification.

Key takeaways

  • lncRNA qPCR assays are essential for RNA-seq validation
  • low expression and isoform complexity require high specificity
  • validated assays improve reproducibility and accuracy
  • qPCR remains the gold standard for lncRNA validation

Why choose AnyGenes® for lncRNA qPCR assays?

  • Assays designed and validated by experienced scientists
  • Proprietary lncRNA database continuously updated with the latest scientific publications and discoveries
  • High specificity for complex RNA targets
  • Proven reproducibility in research applications
  • Personalized technical support

Frequently asked questions

What are LncRNA qPCR assays used for?

They are used to quantify lncRNA expression levels and validate gene expression data, particularly after RNA-seq experiments.

Why are lncRNAs difficult to analyze by qPCR?

Because of low expression, isoform diversity, and potential overlap with coding genes, which can lead to non-specific amplification.

How to ensure specificity in lncRNA qPCR assays?

By using validated primers, targeting exon junctions, and optimizing assay conditions.

Are lncRNA qPCR assays required after RNA-seq?

Yes. qPCR validation is essential to confirm RNA-seq results and ensure accurate expression analysis.

Need support for your lncRNA expression analysis or RNA-seq validation project?

Whether you are validating RNA-seq results, working with low-expression targets, or exploring new biomarkers, AnyGenes provides reliable and experimentally validated lncRNA qPCR assays and dedicated scientific support tailored to your research needs..

Contact our team to discuss your project.