Transcriptomics with Long-Read Sequencing

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Transcriptomics with Long-Read Sequencing

Transcriptomics with RNA and DNA.

RNA sequencing (RNA-seq) using long-read sequencing is a powerful tool for understanding the cell or tissue transcriptome. CD Genomics is a leading global life sciences company, and we continue to expand our services and improve our existing resources to help scientists accelerate their research and support their careers. Here, we offer advanced long-read sequencing platforms (PacBio Iso-Seq and ONT nanopore RNA sequencing) to meet accurate and comprehensive transcriptome profiling. Importantly, our services are highly customized. Based on advanced platforms and years of experience in transcriptome analysis, we are committed to providing the best strategy to meet the project needs of our global clients.

Overview of Transcriptome Analysis

RNA sequencing (RNA-seq) usually refers to the use of NGS technology to comprehensively and rapidly study the sequence information and dynamic expression information of almost all transcripts (including mRNA, rRNA, tRNA, etc.) of eukaryotic cells or tissues in specific conditions. It performs transcriptome analysis, including accurately analyzing gene expression differences, gene structure variation, RNA editing, identifying alternative splicing and fusion genes, discovering new genes, etc. Short-read RNA-seq, such as Illumina technology, is able to quantify gene expression in time and space and has been widely used for biological research. Although short-read RNA-seq can generate large amounts of sequence data, RNA and cDNA fragmentation is required during sample preparation. In addition, their short read is the main limitation, which will result in some information being lost from the original full-length transcripts and therefore are not suitable for transcriptome assembly and isoform detection. With the rapid development of sequencing technologies, long-read sequencing technologies have greatly increased read lengths compared to traditional sequencing technologies and can be applied to address a wide variety of research questions.

Introduction of Long-Read Sequencing (LRS) Technologies

At present, there are two technologies currently dominating the long-read sequencing space, namely Pacific Biosciences' (PacBio) single-molecule real-time (SMRT) sequencing and Oxford Nanopore Technologies' (ONT) nanopore sequencing. The two long-read sequencing technologies rely on different principles. Nanopore sequencers, including MinION, GridION, and PromethION, identify the sequence of bases by measuring the ionic current fluctuations as single-stranded nucleic acids pass through biological nanopores. SMRT sequencers, including RSII, Sequel, and Sequel II, use a fixed polymerase to restrict the replication of DNA to a microwell (zero-mode waveguides, ZMW) and add fluorescent tracer markers to different bases that emit flashes of different colors when the fluorescently labeled nucleotides synthesize the DNA strand.

Table1. Data type, length, accuracy, throughput across long-read and short-read technologies and platforms.

Sequencing technology Platform Data type Read length (kb) Read accuracy (%) Throughput per flow cell (Gb)
      n50 Maximum   Mean Maximum
Pacific Biosciences (PacBio) RS II Continuous long read (CLR) 5–15 >60 87–92 0.75–1.5 2
Sequel Continuous long read (CLR) 25-50 >100 5–10 20
Sequel II Continuous long read (CLR) 30–60 >200 50–100 160
HiFi read 10–20 >20 >99 15–30 35
Oxford Nanopore Technologies (ONT) MinION/ GridION Long read 10–60 >1,000 87–98 2-20 30
Ultra-long read 100–200 >1,500 0.5–2 2.5
PromethION Long read 10–60 >1,000 50–100 180
Illumina NextSeq 550 Single-end 0.075–0.15 0.15 >99.9 16–30 >30
Paired-end 0.075–0.15 (×2) 0.15 (×2) 32–120 >120
NovaSeq 6000 Single-end 0.05–0.25 0.25 65–3,000 >3,000
Paired-end 0.05–0.25 (×2) 0.25 (×2)    

(Logsdon, G. A., et al., 2020)

Services Offering at CD Genomics

Based on PacBio's Single Molecule, Real-Time (SMRT) Sequencing technology, the average read length can now reach 80 Kb, which is already longer than the length of typical genes in the general transcriptome. Therefore, using this long-read-length sequencing platform for transcriptome research, full-length transcript information can be obtained directly without assembly, thus ensuring the accuracy of transcriptome sequencing results to a greater extent.

Besides Pacbio RNA sequencing services, we also offer Oxford nanopore RNA sequencing services. Nanopore RNA sequencing technology enables accurate analysis of full-length native RNA or cDNA without the need to amplify or fragment, streamlining analysis and eliminating amplification bias and read length limitations. More importantly, it is currently the only technology that provides the ability to sequence native RNA strands directly.

Advantages of Long-Features and Benefits of Our Services

  • Years of experience in long-read RNA sequencing.
  • Cutting-edge bioinformatics data analysis.
  • Customized service to customer satisfaction.
  • Customer service representatives are on call 24 hours a day, Monday through Friday.

CD Genomics is dedicated to providing fast and reliable transcriptome sequencing and analysis services for humans, animals, plants, and so on. If you are interested in our services, please discuss your research with one of our professional scientists.


  1. Oikonomopoulos, S., et al. (2020). "Methodologies for transcript profiling using long-read technologies." Frontiers in genetics, 606.
  2. Amarasinghe, S. L., et al. (2020). "Opportunities and challenges in long-read sequencing data analysis." Genome biology, 21(1), 1-16.
  3. Logsdon, G. A., et al. (2020). "Long-read human genome sequencing and its applications." Nature Reviews Genetics, 21(10), 597-614.
For Research Use Only. Not for use in diagnostic procedures.

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