Single-cell sequencing
... long-read sequencing not only matched the gene expression and cell-type annotation performance of short-read sequencing but also excelled in the precise identification of transcript isoforms
Wang, M. et al. bioRxiv (2024)
Reveal more biology — gene and isoform expression, plus variant detection in a single experiment
Prepare samples efficiently: approximately three hours from cDNA to sequencing
Analyse data with intuitive EPI2ME workflow, including barcode and UMI demultiplexing — no short reads required
Ultra-rich single-cell transcriptome data without compromise
The analysis of transcriptomic heterogeneity at the single-cell level has provided new insights into many research areas, including cancer research, cell development and function, and immunology. However, the use of traditional short-read sequencing technology limits the ability to identify transcript abundance at the isoform level. Nanopore reads of unrestricted length resolve this challenge, enabling the sequencing of full-length transcripts to gain a deeper understanding of complex biology. Oxford Nanopore provides an end-to-end solution for single-cell RNA sequencing — from library preparation in approximately three hours, through to intuitive single-cell analysis with EPI2ME.
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Single-cell transcriptomics workflow
Learn about the complete workflow for single-cell transcriptome analysis, starting from 10x Genomics cDNA, through to approximately three hour library prep and high-output sequencing on PromethION, and finishing with data analysis using EPI2ME.
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Transcript isoform detection with single-cell resolution
Discover how, by combining 10x Genomics assays and nanopore reads of unrestricted length, researchers can measure differential gene expression of alternative transcript isoforms and cluster spatial expression data or cells by gene and isoform expression with single-cell resolution.
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PromethION 24
A flexible device for large-scale single-cell transcriptome sequencing on up to 24 independently addressable PromethION Flow Cells, providing scalability from low to high throughput. Leverage state-of-the-art algorithms and GPU technology with high-performance onboard compute.
EPI2ME wf-single-cell
The dedicated wf-single-cell pipeline enables the direct demultiplexing of single-cell barcoded reads without the need for paired short-read data. The workflow extracts cell barcodes and unique molecular identifiers (UMIs) to output gene, genotype, and isoform count matrices, UMAP plots, and a BAM file of aligned reads.
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Flexible, affordable, high-output nanopore devices for every lab — in a compact, accessible form.
Technology comparison
Oxford Nanopore sequencing
Legacy short-read sequencing
Any read length (50 bp to >4 Mb)
Short read length (<300 bp)
- Generate complete, high-quality genomes with fewer contigs and simplify de novo assembly
- Resolve genomic regions inaccessible to short reads, including complex structural variants (SVs) and repeats
- Analyse long-range haplotypes, accurately phase single nucleotide variants (SNVs) and base modifications, and identify parent-of-origin effects
- Sequence short DNA fragments, such as amplicons and cell-free DNA (cfDNA)
- Sequence and quantify full-length transcripts to annotate genomes, fully characterise isoforms, and analyse gene expression — including at single-cell resolution
- Resolve mobile genetic elements — including plasmids and transposons — to generate critical genomic insights
- Enhance taxonomic resolution using full-length reads of informative loci, such as the entire 16S gene
- Assembly contiguity is reduced and complex computational analyses are required to infer results
- Complex genomic regions such as SVs and repeat elements typically cannot be sequenced in single reads (e.g. transposons, gene duplications, and prophage sequences)
- Transcript analysis is limited to gene-level expression data
- Important genetic information is missed
Direct sequencing of native DNA/RNA
Amplification required
- Eliminate amplification- and GC-bias, along with read length limitations, and access genomic regions that are difficult to amplify
- Detect epigenetic modifications, such as methylation, as standard — no additional, time-consuming sample prep required
- Create cost-effective, amplification-free, targeted panels with adaptive sampling to detect SVs, repeats, SNVs, and methylation in a single assay
- Amplification is often required and can introduce bias
- Base modifications are removed, necessitating additional sample prep, sequencing runs, and expense
- Uniformity of coverage is reduced, resulting in assembly gaps
Real-time data streaming
Fixed run time with bulk data delivery
- Analyse data as it is generated for immediate access to actionable results
- Stop sequencing when sufficient data is obtained — wash and reuse flow cell
- Combine real-time data streaming with intuitive, real-time EPI2ME data analysis workflows for deeper insights
- Time to result is increased
- Workflow errors cannot be identified until it is too late
- Additional complexities of handling large volumes of bulk data
Accessible and affordable sequencing
Constrained to centralised labs
- Sequence on demand with flexible end-to-end workflows that suit your throughput needs
- Sequence at sample source, even in the most extreme or remote environments, with the portable MinION device — minimise potential sample degradation caused by storage and shipping
- Scale up with modular GridION and PromethION devices — suitable for high-output, high-throughput sequencing to generate ultra-rich data
- Sequence as and when needed using low-cost, independently addressable flow cells — no sample batching needed
- Use sample barcodes to multiplex samples on a single flow cell
- Bulky, expensive devices that require substantial site infrastructure — use is restricted to well-resourced, centralised locations, limiting global accessibility
- High sample batching is required for optimal efficiency, delaying time to results
Streamlined, automatable workflows
Laborious workflows
- Prepare samples in as little as 10 minutes, including multiplexing
- Use end-to-end whole-genome, metagenomic, targeted (including 16S barcoding), direct RNA and cDNA sequencing workflows
- Scale and automate your workflows to suit your sequencing needs
- Perform real-time enrichment of single targets or panels without additional wet-lab prep by using adaptive sampling
- Lengthy sample prep is required
- Long sequencing run times
- Workflow efficiency is reduced, and time to result is increased
