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RNA and gene expression analysis using direct RNA and cDNA sequencing

Unlike traditional RNA-Seq techniques, long nanopore RNA sequencing reads allow for accurate quantification and complete, full-length characterisation of native RNA or cDNA without fragmentation or amplification — streamlining analysis and removing potential sources of bias. Direct RNA sequencing also enables the identification of base modifications alongside nucleotide sequence.

  • Characterise and quantify full-length transcripts — up to single-cell resolution
  • Get faster access to results with real-time analysis and bespoke tools
  • Reduce bias with PCR-free protocols
  • Explore epigenetic modifications through direct RNA sequencing
  • Scale to your needs using Flongle, MinION, GridION or PromethION

How will you use nanopore technology?

Quantify and study differential gene expression

Identify fusion transcripts

Characterise RNA viruses and viral epidemiology

Detect base modifications

The high yields of long, full-length reads delivered by nanopore sequencing allow unambiguous characterisation and quantification of transcript isoforms – providing a true reflection of gene expression. Low input amounts combined with rapid, streamlined workflows enable highly sensitive gene expression analysis, even from single cells.

With nanopore sequencing, read length is equal to fragment length, enabling routine analysis of long, full-length transcripts. This minimises the impact of multimapping — where short sequencing reads align to multiple locations — and allows complete characterisation of transcript isoforms and chimeric transcripts. Phasing can also be determined, providing easy differentiation between clonal and polyclonal variants. 

  • Unambiguous identification of full-length fusion transcripts, including where one fusion partner is unknown
  • Accurate transcript quantification
  • Rapid, real-time sequencing and analysis
  • Eliminate PCR bias using direct cDNA or direct RNA sequencing
  • A simple, cost-effective, and scalable solution for any lab 

‘Multi-modality of nanopore is a huge asset — methylation, SV, gene fusions, single mutations and phasing — it’s amazing to have all that in the single assay’

Abderouf Hamza, Institut Curie, France

Christina Stangl: Partner-independent fusion gene detection by multiplexed CRISPR/Cas9 enrichment and long-read sequencing

Rapid characterisation of RNA viruses – at the bench or in the field – using real-time, long nanopore RNA sequencing reads. 

  • Full viral RNA sequence in one read – no need to assemble
  • Long reads enhance viral identification from metagenomic samples
  • Portable device and kits for rapid, field-based analysis
  • Real-time analysis delivers immediately actionable results
  • Cost-efficient sample multiplexing options

Base modifications such as m6A can modulate the activity and stability of RNA molecules, and have been linked to multiple human diseases and antimicrobial resistance. Unlike traditional technologies, nanopore technology can sequence native RNA molecules. With no requirement for amplification or reverse transcription, nanopore sequencing allows direct identification of base modifications alongside the nucleotide sequence — no chemical or protocol adaptations are required. The facility to sequence full-length transcripts enables modifications to be unambiguously assigned to specific isoforms.

  • Cost-effectively identify RNA base modifications alongside nucleotide sequence
  • Capture base modifications as standard — analyse when you are ready
  • Unambiguously assign base modifications to transcript isoforms using long, full-length reads
  • Streamlined protocol with no harsh or inefficient chemical adaptations required — maintain the integrity of your RNA molecules and data
  • Analyse data using Tombo, one of a growing number of tools

‘The establishment of the [Oxford Nanopore] platform as a tool to map virtually any given modification will allow us to query the epitranscriptome in ways that, until now, had not been possible’

Liu et al

Eva Maria Novoa: Decoding the epitranscriptome at single-molecule resolution

Choose your RNA sequencing kit

  Direct RNA Sequencing Kit cDNA-PCR Sequencing Kit Direct cDNA Sequencing Kit
Preparation time 105 mins 165 mins 275 mins
Input requirement 500 ng total RNA or 50 ng poly-A+ RNA 1 ng RNA (poly-A+) 100 ng RNA (poly-A+)
RT required Optional Yes Yes
PCR required No Yes No
Read length Equal to RNA length Enriched for full-length cDNA Enriched for full-length cDNA
Typical throughput
Typical number of reads (MinION, 1 kb avg. length) 1 million 7 - 12 million 5 - 10 million
Typical number of reads (PromethION, 1 kb avg. length) 8 million > 60 million 30 - 60 million
Multiplexing options In development PCR Barcoding Kit Native Barcoding Kit
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