The PromethION 2 (P2) Solo by Oxford Nanopore is a compact benchtop sequencer designed to run up to two independently addressable PromethION flow cells, allowing experiments to be conducted simultaneously or separately for greater flexibility. The UMGC has built a highly capable control computer to operate the P2 Solo and perform onboard analysis.
Nanopore sequencing differs from optical-based platforms by passing DNA or RNA through a membrane-bound protein nanopore under an electrical voltage, with ionic current fluctuations decoded in silico. Unlike other technologies, Nanopore enables direct RNA sequencing without cDNA synthesis and has no theoretical read-length limit, allowing for mappable reads over 1 Mbp.
With ultra-long read capabilities, Nanopore sequencing enhances genome assembly, structural variant detection, and full-length RNA transcript sequencing, while preserving long-range methylation data without the need for fragmentation or amplification.
Applications:
- Flexible sequencing of whole genomes, targeted regions, and full-length RNA transcripts
- Quantify and characterize RNA splice variants, isoforms, and fusion transcripts
- Directly identify epigenetic modifications (e.g. methylation) alongside nucleotide sequence
- Isoform-level expression from full-length cDNA sequencing prepared from 10x libraries
- Long reads enhance the analysis of repetitive regions, structural variation, and more
Self-service
Sequencing on the Nanopore P2 Solo is only available as a self-service option in the UMGC CoLab. Researchers receive training in library preparation, quality assessment, instrument operation, and basic run analysis. Researchers provide their own library preparation reagents and flow cells for their chosen application, with DNA flow cells available for purchase from the CoLab.
Output
The output of the Promethion flow cell is up to 250 Gb of data, depending on the library type and application. Typical output for standard WGS libraries is 100-120 Gb when input DNA is sheared and size-selected.
Benefits
- Ultra-long Reads: With the potential for ultra-long read lengths up to 2 MB, investigators can assemble complex genomes and resolve repetitive regions that are difficult for short-read technologies.
- High Accuracy: a full suite of supported polishing tools routinely give consensus accuracy >QV40 (99.99%), with improvements to base callers being rolled out regularly.
- Uniform Coverage: No bias based on GC content enables sequencing through regions inaccessible to other technologies. Template preparation and sequencing do not rely on amplification. Thus, there is no PCR bias for more uniform genome coverage.
- Epigenetics: With no PCR amplification step, base modifications are directly detected during sequencing without the need for bisulfite conversion.
- Direct RNA Sequencing: Allows the sequencing of native RNA molecules without fragmentation or amplification for unbiased, full-length transcript isoform sequences.
Getting Started
The CoLab is a co-working space within the UMGC that provides shared access to our lab and instruments, and training in genomic methods. If you are interested in training on the P2 Solo, contact Aaron Becker, the CoLab Lead, at [email protected].
The P2 solo is only available as a self-serve device in the CoLab setting.
UMN researchers
- Currently, there is no cost to use the P2 Solo instrument or CoLab bench space.
- Training on the P2 Solo is provided at no cost.
- Researchers are responsible for providing library preparation reagents and enzymes.
- The CoLab will keep a small # of Promethion DNA flow cells on hand for purchase. RNA flow cells will be provided on an as-needed basis. Promethion flow cells are available for purchase directly from Nanopore.
- The CoLab will provide flow cell wash and priming reagents for washing and re-loading Promethion flow cells.
External researchers
Outside organizations and universities can access the CoLab and will be charged a training and instrument usage fee.
Location
The P2 Solo is housed in the UMGC CoLab space. The CoLab is located at 1-210 Cancer and Cardiovascular Research Building (2231 6th St SE, Minneapolis, MN 55455) on the East Bank of the University of Minnesota.
Additional location details:
- Building access: A Ucard is needed to enter the CCRB building.
- Lab location: Using the main CCRB entrance, the 1-210 CCRB lab is the first hallway on the left and the second door on the left.
Training
Training is required to use the P2 Solo and receive Ucard access to the lab. New users will begin with an orientation to the CoLab and can schedule an orientation time here. After orientation, a separate time will be scheduled to train on the P2 solo instrument. If you have general questions about the CoLab and training, contact Aaron Becker, the CoLab Lead, at [email protected].
CoLab
The CoLab is located within the UMGC’s CCRB facility and features dedicated, fully equipped lab benches for individual use and 1,000 square feet of amenities, standard equipment, specialized instrumentation, and freezer storage. Altogether, UMGC staff have decades of technical experience and extensive knowledge of instrumentation and workflows to share. Training and bench space access are provided at no cost to UMN researchers.