The Health Sciences Center DNA Sequencing Core at the University of Utah provides options for sequencing to members of the university community and surrounding areas. Their services offer sequencing through the use of multiple methodologies:
- Short read sequencing on the Element Biosciences AVITI
- Long read sequencing with Oxford Nanopore Technologies (ONT)
- Single-cell sequencing with the 10x Genomics Chromium Controller
- Sanger sequencing on the Applied Biosystems 3730xl
Element Biosciences AVITI
The Element Biosciences AVITI is a recently purchased, cutting-edge instrument in the short-read market. The AVITI is a mid-sized sequencer, so flow cells provide approximately 1 billion reads per run or less. This makes it ideal for rapid turnaround times on projects. Typically sequencing runs can be done from library receipt to data delivery in a matter of days. This instrument provides reads that are mostly in the Q40 range rather than the historically standard Q30 output, providing exceptional data quality from samples.
The AVITI is also more tolerant of GC composition than standard sequencing. This allows for better sequencing overall as coverage will be more uniform across templates, especially difficult templates. The AVITI is also able to sequence through difficult regions—such as homopolymer stretches—and then continue to provide usable sequences afterward.
Oxford Nanopore Technologies (ONT)
Oxford Nanopore Technologies (ONT) technology provides multiple sequencing options, affording the ability to answer multiple questions. The P2Solo instrument the core recently received can run two PromethION flow cells at once. Each flow cell is sufficient to sequence one human genome. Smaller projects can be barcoded and combined into a single run.
The instrument will sequence the DNA and can also obtain the methylation state of the DNA at the same time. Because it is based on a pore rather than an enzymatic method, the ONT devices are the only systems on the market that can directly read RNA.
The ONT system also has the unique ability to allow for the sequencing of primarily regions of interest and throw out reads from areas outside the targeted regions. This mode is called adaptive sampling. A bed file is created with some buffer areas around your target regions. This bed file informs the sequencer which sequences are targeted. In this way, target regions can be enriched during the run without any special captures or amplification approaches.
10x Genomics Chromium Controller
The 10x Genomics Chromium Controller is used for single-cell analysis. Researchers are using this to evaluate cell types from different organs. The controller can be used for all 10x protocols except spatial and fixed cells at this time. The DNA Sequencing core works hand in hand with the HSC Flow Cytometry core and HSC Bioinformatics core to provide a sample-to-data experience for our users.
Applied Biosystems 3730xl
The ABI 3730xl is the workhorse that has been used in the industry for many years and continues to put out quality data for researchers here on campus and surrounding areas. Turnaround time on samples can be as quick as the same day.
In addition to the above, the DNA Sequencing core is always interested in helping with experiments that may not fit into the standard box envisioned by manufacturers of instrumentation and as such is always willing to discuss and help execute plans for novel and exciting additions to the technologies and techniques already in use in our core. Feel free to contact core personnel about your project.
Contact Derek Warner (dwarner@cores.utah.edu) for further information or with any questions.
