Nanopore Direct RNA Sequencing

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Nanopore Direct RNA Sequencing

RNA molecule.

Oxford nanopore RNA sequencing (RNA-seq) technology enables accurate analysis of full-length transcripts without the need to amplify or fragment, streamlining analysis and eliminating amplification bias and read length limitations. More importantly, Oxford Nanopore Technology (ONT) is the first long-read technique capable of directly sequencing native RNA strands. CD Genomics is now providing nanopore direct RNA ( direct cDNA or direct RNA)sequencing to achieve the ultimate goal of a comprehensive and bias-free understanding of transcriptomes. With years of experience in long-read RNA-seq analysis and advanced ONT platforms, we will be your best partner for direct RNA-seq.

Features of Nanopore Direct RNA Sequencing

To date, direct RNA-seq has been used in the study of various species, including Caenorhabditis elegans, Arabidopsis, yeast, and human cell lines. Compared with other sequencing technologies, nanopore direct RNA sequencing has its unique advantages, including,

  • Direct RNA sequencing with amplification-free protocols.
    The PCR process has GC bias and it is not easy to amplify sequences with too high or too low GC content. Short-read sequencing needs to introduce GC preference during library building and sequencing, which reduces the accuracy of quantitative analysis. Using ONT sequencing technology, unbiased, full-length, and strand-specific RNA sequences can be obtained without PCR amplification or fragmentation steps.
  • Provide transcript poly-A tail length estimations.
    The transcript poly-A tail is believed to play an important role in post-transcriptional regulation, including mRNA stability and translation efficiency. The poly-A tails can be hundreds of nucleotides in length and are difficult to measure using short-read sequencing. The full-length transcripts obtained by ONT direct RNA sequencing contain poly-A tail information. The method can not only estimate the poly-A tail length for each RNA but also has the potential to detect differences in poly-A tails between isomers.
  • Cost-effective identification of RNA base modifications alongside nucleotide sequence.
    Direct RNA sequencing does not require amplification or synthesis steps, modified bases pass directly through the nanopore, producing a different current signature in the original signal than bases that have not been modified. Information on base modifications can be detected by identifying current features through specific software algorithms.

Our Service Workflow

Our Service Workflow -CD Genomics

Sample Requirements

  • Sample type: Blood, tissues, cells, RNA samples and more.
  • Library construction strategy and sample requirements:

-Direct RNA sequencing: RNA amount ≥1μg, RNA-integrity scores (RIN-scores) ≥ 8.

-Direct cDNA sequencing: RNA amount ≥ 1μg, RNA-integrity scores (RIN-scores) ≥ 8.

-The RNA samples need to be DNA-free and need to be accompanied by Bioanalyzer traces.

-Our Service Support

Different types of library preparation protocols can be used for direct cDNA/RNA sequencing. Real-time streaming of sequence data allows for fast insight into samples, on-demand sequencing, and dynamic workflows. Our service support,

-Classification of known and novel transcripts.

-Characterization of poly-A tail lengths of individual transcripts.

-Identification of allele-specific gene and complex RNA splice isoforms.

-Identification of RNA base modifications and RNA structure prediction.

-Quantify and study differential gene expressions.

-Characterization of RNA viruses and viral epidemiology.

Thanks for your interest in our services. Please feel free to contact us. We’ve got everything covered for your needs and looking forward to hearing from you.


  1. Vacca, D., et al. (2022). "Direct RNA nanopore sequencing of SARS-CoV-2 extracted from critical material from swabs." Life, 12(1), 69.
  2. Soneson, C., et al. (2019). "A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes." Nature communications, 10(1), 1-14.
For Research Use Only. Not for use in diagnostic procedures.

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