Oxford Nanopore Technologies announces new collaboration with 10x Genomics to make single-cell and spatial full-length isoform transcript sequencing accessible to any laboratory

New end-to-end, single-cell nanopore-based sequencing solution brings an easy and affordable option for full-length isoform single-cell and spatial sequencing to enable the exploration of new biology.

New insights possible with single-cell and spatial nanopore sequencing

Oxford Nanopore Technologies plc (Oxford Nanopore) today announces a collaboration with 10x Genomics, to enable a streamlined workflow for sequencing full-length transcripts in single reads on highly accessible Oxford Nanopore devices. This will provide users with the ability to span features such as fusion genes or transcripts with repetitive regions, producing abundant, cost-effective single-cell and spatial sequencing data.

The collaboration covers the addition of Oxford Nanopore’s PromethION devices and selected consumables, in conjunction with sample preparation on the 10x Genomics devices, into the 10x Genomics Compatible Partner Program (CPP). Alongside this, Oxford Nanopore has also released a new openly available end-to-end nanopore-only single-cell protocol. Both parties believe this will enable a streamlined customer experience and highlight the compelling utility of nanopore-based sequencing in conjunction with 10x Genomics workflows.

The analysis of genomic and transcriptomic heterogeneity at the single-cell level has provided new insights into many research areas, including cancer research, cell biology, embryonic development and immunology. However, the use of traditional short-read sequencing technology can leave certain types of information like isoform-specific transcript abundance invisible to researchers. Additionally, the 10x Genomics App Note outlines how data on cell calling and clustering from sequencing long fragments is comparable to short reads and, upon further analysis of data from sequencing long fragments, it was possible to accurately identify isoforms differentially expressed between cell types.

Nanopore sequencing reads resolve these challenges, enabling end-to-end sequencing of full-length transcripts in single reads, which span features such as fusion genes or transcripts with repetitive regions. By combining the power of 10x Genomics’ single-cell and spatial assays with nanopore sequencing, researchers have a powerful new tool to see unique differences in isoform expression, alternative splicing, cellular sub-types, immune receptor profiling, spatial transcriptomics, and other emerging applications.

The Oxford Nanopore products listed in the 10x Genomics CPP include PromethION devices, flow cells and kits. In addition to these products, which are compatible with 10x Genomics assays, a new openly available nanopore-only protocol means that customers do not need to use lengthy or complex sequencing workflows in order to see isoform information, which can take up to two or three days with other traditional sequencing methods, and even some newer approaches. Now, with Oxford Nanopore, 10x Genomics users can easily add a new dimension to their data using the fastest and most cost-effective full-length transcript sequencing approach.

Single-cell and spatial analysis well suited for PromethION devices

As single-cell and spatial analyses can be incredibly data-intensive and complex, they are ideally suited for Oxford Nanopore’s PromethION Flow Cells and devices, which are capable of the highest levels of sequencing throughput. A typical single-cell atlas project is similar to a population genomics study in order of magnitude of data, where a whole transcriptome is produced for every individual cell in a sample. Oxford Nanopore will now offer the highest throughput full-length sequencing option for single-cell sequencing at over 80 million full-length cell-assigned reads per PromethION Flow Cell.

In an ongoing mission to improve accessibility to human genomics, Oxford Nanopore yesterday announced the roll out of its PromethION 2 (P2) Solo sequencer, the world’s most accessible, high-yield sequencing device with the potential to greatly expand access to accurate, fast and affordable sequencing for human genetics and other larger datasets. With a starter pack beginning at USD$10,455, the P2 Solo device is the only small, high-yield sequencer on the market, and this will allow anyone to move beyond basic DNA analysis by incorporating more comprehensive analysis. The P2 Solo can run two high-yield PromethION Flow Cells independently, which are well suited for single-cell and spatial transcriptomics.

Now, with Oxford Nanopore, researchers using 10x Genomics have the option to streamline their single-cell and spatial experiments, conducting sample prep and sequencing, without having to wait. Oxford Nanopore also offers a PromethION 24 and PromethION 48, both of which are capable of much higher order of magnitude in throughput and can be employed for larger single-cell atlas projects. Oxford Nanopore’s devices utilise high-accuracy nanopore sequencing of any-length native reads to improve the resolution of results, opening the genomics market by equipping anyone, anywhere with high-yield whole genome sequencing data within hours rather than days or weeks.

Gordon Sanghera, CEO, Oxford Nanopore Technologies, commented:

“Our range of accessible, high-throughput nanopore devices makes single-cell sequencing accessible to every laboratory. We are proud to be collaborating with 10x Genomics to enable greater discoveries in human genomics with the ability to explore new dimensions of biology with single-cell nanopore sequencing. Full-length single-cell and spatial transcripts are revealing new information that has never been seen before, and this is made possible by Oxford Nanopore’s ability to deliver this readout at very high throughput.”

Edwin Hauw, VP of Marketing, 10x Genomics, commented:

“Single-cell analysis is driving new insights and discoveries across biology, yet there are so many more research questions waiting to be answered and new application areas that can be unlocked. The 10x Genomics Compatible Partner Program helps make our comprehensive suite of single-cell and spatial tools more accessible to the global research community. We're excited to welcome Oxford Nanopore to the 10x Compatible Partner Program and to validate our leading Chromium single-cell and Visium spatial portfolio for use on PromethION devices. This collaboration enables high-throughput sequencing of full-length single-cell and spatial libraries, helping researchers explore biology in new ways by obtaining alternative transcript isoform expression with single-cell and spatial resolution.”

Added scientific value

Nanopore sequencing provides added value to 10x Genomics users by leveraging the capability to read any-length of native DNA/RNA fragment to add more breadth to their single-cell and spatial transcriptomics research:

• Discover isoform diversity

• Identify SNPs fusions anywhere in a gene

• Comprehensive immune profiling

• Full-length spatial transcriptomics

• Accurate single-cell gene expression

Interested scientists and researchers can learn more about Oxford Nanopore single-cell and spatial sequencing with 10x Genomics by using the resources below:

• 10x Genomics App Note

• Oxford Nanopore single-cell protocol

• 10x Genomics sample data sets:

- Chromium 3’ Single Cell Gene Expression

- Chromium 5’ Single Cell Gene Expression

- Visium Spatial Gene Expression

• Oxford Nanopore single-cell workflow

Attendees of the American Society of Human Genetics Conference (ASHG) held in Los Angeles this week can attend the Oxford Nanopore Workshop to learn more:

• Unravelling complex human genomes – one sequencing platform for all your biology

- Danny E. Miller, University of Washington and Seattle Children's Hospital

- Fritz Sedlazeck, Baylor College of Medicine and Rice University

- Carolyn A. Morrison, 10x Genomics

- Rosemary Sinclair Dokos, Oxford Nanopore Technologies

• Lunch Seminar: Thursday, October 27, 12:30 PM – 1:30 PM, Theater 411

• Register here.