While NGS-based mRNA sequencing is a versatile tool for quantifying gene expression, its reliance on short reads restricts its efficacy in complex transcriptomic analyses. On the other hand, nanopore sequencing employs long-read technology, enabling the sequencing of full-length mRNA transcripts. This approach facilitates a comprehensive exploration of alternative splicing, gene fusions, poly-adenylation, and the quantification of mRNA isoforms.

Nanopore sequencing, a method that relies on nanopore single-molecule real-time electrical signals, provides results in real-time. Guided by motor proteins, double-stranded DNA binds to nanopore proteins embedded in a biofilm, unwinding as it passes through the nanopore channel under a voltage difference. The distinctive electrical signals generated by different bases on the DNA strand are detected and classified in real-time, facilitating accurate and continuous nucleotide sequencing. This innovative approach overcomes short-read limitations and provides a dynamic platform for intricate genomic analysis, including complex transcriptomic studies, with immediate results.

Platform: Nanopore PromethION 48

  Features

  Capture of poly-A mRNA followed by cDNA synthesis and library preparation
  Sequencing of the full-length transcripts
  Bioinformatic analysis based on alignment to a reference genome
  Bioinformatic analysis includes not only expression at gene and isoform-level but also analysis of lncRNA, gene fusions, poly-adenylation and gene structure

  Service Advantages

    Quantification of expression at the isoform level: enabling detailed and accurate expression analysis, unveiling change that may be masked when analysing the whole gene expression

  Reduced Data Demands: Compared to Next-Generation Sequencing (NGS), Nanopore sequencing exhibits lower data requirements, allowing for equivalent levels of gene expression quantification saturation with smaller data.

  Higher accuracy of expression quantification: both at gene and isoform level

  Identification of additional transcriptomic information: alternative polyadenylation, fusion genes and lcnRNA and their target genes

  Extensive Expertise: Our team brings a wealth of experience to every project, having completed over 850 Nanopore full-length transcriptome projects and processed over 8,000 samples.

  Post-Sales Support: our commitment extends beyond project completion with a 3-month after-sale service period. During this time, we offer project follow-up, troubleshooting assistance, and Q&A sessions to address any queries related to the results.

  Sample Requirements and Delivery

  Sample Requirements:
Nucleotides:

- Plants:
   Root, Stem or Petal: 450 mg
   Leaf or Seed: 300 mg
   Fruit: 1.2 g

- Animal:
   HEart or Intestine: 300 mg
   Viscera or Brain: 240 mg
   Muscle: 450 mg
   Bones, Hair or Skin: 1g

- Arthropods:
   Insects: 6g
   Crustacea: 300 mg

- Whole blood: 1 tube

- Cells: 106 cells

  Service Work Flow
Nucleotides:

Sample delivery	Library construction	Sequencing	Data analysis	After-sale services

  Service Work Flow

Experiment design	Sample delivery	RNA extraction	Library construction	Sequencing	Data analysis	After-sale services

-  Raw data processing
-  Transcript identification
-  Alternative splicing
-  Expression quantification in gene level and isoform level
-  Differential expression analysis
-  Function annotation and enrichment (DEGs and DETs)

Alternative splicing analysis

Alternative Polyadenylation Analysis (APA)

lncRNA prediction

Annotation of novel genes

Clustering of DETs

Protein-Protein Networks in DEGs

Explore the advancements facilitated by BMKGene’s Nanopore full-length mRNA sequencing services through a curated collection of publications.

Gong, B. et al. (2023) ‘Epigenetic and transcriptional activation of the secretory kinase FAM20C as an oncogene in glioma’, Journal of Genetics and Genomics, 50(6), pp. 422–433. doi: 10.1016/J.JGG.2023.01.008.

He, Z. et al. (2023) ‘Full-length transcriptome sequencing of lymphocytes respond to IFN-γ reveals a Th1-skewed immune response in flounder (Paralichthys olivaceus)’, Fish & Shellfish Immunology, 134, p. 108636. doi: 10.1016/J.FSI.2023.108636.

Ma, Y. et al. (2023) ‘Comparative analysis of PacBio and ONT RNA sequencing methods for Nemopilema Nomurai venom identification’, Genomics, 115(6), p. 110709. doi: 10.1016/J.YGENO.2023.110709.

Yu, D. et al. (2023) ‘Nano-seq analysis reveals different functional tendency between exosomes and microvesicles derived from hUMSC’, Stem Cell Research and Therapy, 14(1), pp. 1–13. doi: 10.1186/S13287-023-03491-5/TABLES/6.