Whole-transcriptome sequencing
Gain a comprehensive view of whole transcriptomes with high-output nanopore sequencing of full-length transcripts. Unambiguously identify and quantify isoforms and detect fusion genes. Discover new biology with the power of single-cell sequencing. Detect base modifications and avoid PCR bias with nanopore direct RNA sequencing — the only technology enabling direct sequencing of native RNA molecules.
What is whole-transcriptome sequencing?
Whole-transcriptome sequencing enables the analysis of the RNA transcripts present in a sample from an organism of interest. The method provides a dynamic view of the cellular activity at the point of sampling, allowing characterisation of gene expression and identification of isoforms. However, accurate analysis of transcripts using traditional short-read sequencing technology can be challenging, as RNA samples must be fragmented, sequenced in short sections, then reassembled, leading to potential multi-mapping — where short sequencing reads align to multiple locations.
With long nanopore reads, full-length transcripts can be sequenced end-to-end, facilitating their accurate, unambiguous analysis. Researchers are using whole-transcriptome sequencing to shed light on developmental biology, study the mechanisms underlying diseases such as cancers, and identify potential future disease-associated biomarkers.
Why nanopore technology for whole-transcriptome sequencing?
Nanopore technology enables complete, isoform-level transcriptome characterisation — at up to single-cell resolution.
Using nanopore sequencing, you can:
- Characterise and quantify full-length transcripts
- Unambiguously identify splice variants and fusion transcripts
- Reveal gene expression heterogeneity with single-cell transcriptomics
- Explore epigenetic modifications through direct RNA sequencing
- Enhance viral identification from metagenomic samples
One platform — comprehensive analysis
Experimental approach to whole-transcriptome sequencing
Sequencing kits are available for the preparation of both RNA and cDNA libraries. The Direct RNA Sequencing Kit allows native RNA molecules — including base modifications — to be sequenced directly. Enabling high-output sequencing of whole transcriptomes from low input amounts, the cDNA-PCR Sequencing Kit is ideal for identifying and quantifying full-length transcripts at the isoform level.
| Sequence RNA molecules directly and preserve base modifications | Identification and quantification of full-length transcripts with highest output | |
|---|---|---|
| Direct RNA Sequencing Kit | cDNA-PCR Sequencing Kit | |
| Preparation time | 105 min | ~210 min + PCR |
| Input requirement | 50 ng poly(A)+ RNA or 500 ng total RNA | 4 ng poly(A)+ RNA or 200 ng total RNA |
| Reverse transcription required | Optional | Yes |
| PCR required | No | Yes |
| Read length | Equal to RNA length | Enriched for full-length cDNA |
| Typical throughput | 1/3 | 3/3 |
| Multiplexing options | In development | Yes |
| Methylation included | Yes | No |
| Buy now | Buy now |
Find out more about whole-transcriptome sequencing
Learn more about the benefits of sequencing full-length transcripts with long nanopore reads and get best-practice recommendations for single-cell sequencing.
Which device for whole-transcriptome sequencing?
From powerful, portable Flongle and MinION devices, suitable for low-pass whole-transcriptome sequencing, to the flexible GridION and high-output PromethION platforms, ideal for isoform-level differential expression analysis — scale your RNA sequencing to match your specific research requirements.
PromethION 2 and PromethION 2 Solo
Offering the flexibility of two independent, high-output PromethION Flow Cells, the compact PromethION 2 devices bring the benefits of high-coverage, real-time nanopore sequencing to every lab. Ideal for low-cost access to highly accurate whole transcriptomes.
Flexible, population-scale sequencing using up to 48 independent, high-capacity flow cells — complete genomic and transcriptomic characterisation of large sample numbers.
Combining up to 24 independently addressable, high-capacity flow cells with powerful, integrated compute, PromethION 24 delivers flexible, on-demand access to terabases of sequencing data — ideal for cost-effective, high-throughput sequencing.
Flexible, high-yield nanopore sequencing for every lab. The PromethION 2 devices are designed to be compact and accessible, utilising two PromethION Flow Cells that can generate hundreds of gigabases of data each.
From genome assembly to gene expression, run multiple experiments on-demand using five independent MinION or Flongle Flow Cells.
Integrated sequencing and analysis in a powerful handheld device — suitable for small animal genomes, targeted sequencing, and gene expression studies.
Adapting MinION and GridION for smaller, routine tests and analyses. Low-plex targeted sequencing, RNA isoform analysis, and quality control applications.
Analysis techniques for whole-transcriptome sequencing
Oxford Nanopore provides end-to-end bioinformatics workflows for the analysis of whole transcriptomes. The workflow wf-transcriptoms enables de novo or reference-guided transcript assembly from either cDNA or direct RNA reads, and provides differential gene expression and differential transcript usage analysis. For single-cell transcriptome analysis, the workflow wf-single-cell, a research pipeline, provides outputs including barcode and unique molecular identifier (UMI) tags, gene x cell expression matrices, and cell x transcript expression matrices. Both workflows are available in EPI2ME Labs.
Find out more about analysing nanopore whole-transcriptome and single-cell transcriptomic sequencing data.
Featured whole-transcriptome sequencing workflow
For high-throughput analysis of whole human transcriptomes, we recommend the following:
Inspiration for whole-transcriptome sequencing
Discover more about applying nanopore whole-transcriptome sequencing to your area of research.
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