Whole-transcriptome sequencing
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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.
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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