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.
- Full-length transcripts — unambiguous identification of splice variants and fusion transcripts
- Accurate transcript and isoform quantification
- Eliminate PCR bias using direct cDNA or direct RNA sequencing
- Detect base modifications alongside nucleotide sequence using direct RNA
- Easy identification of anti-sense transcripts and lncRNA isoforms
‘Our results show that not only can we identify complex isoforms, but also quantify their expression, at the single cell level’
Jeremy Wang: Classification of pediatric acute leukaemia using full-length transcriptomics
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’
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
‘Direct RNA sequencing of a human rhinovirus… This approach has many potential advantages over other RNA-Seq strategies’
Redefining the transcriptional complexity of viral pathogens using direct RNA sequencing
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’
Eva Maria Novoa: Decoding the epitranscriptome at single-molecule resolution
Choose your RNA sequencing kit
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| 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 |  |
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| 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 |
| Buy now | Buy now | Buy now | |