Category Archives: Sequencing

Coming soon: Illumina MiSeq i100

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The CQLS was awarded a 2025 Research Equipment Reserve Fund (RERF) to purchase a new Illumina MiSeq i100.

The CQLS has run an Illumina MiSeq for 12 years as the center of a highly successful low-range sequencing service. Primarily used for microbiome, environmental, and amplicon samples, the MiSeq offers a lower volume of Illumina high-throughput sequencing compared to the CQLS’ Illumina NextSeq. Illumina is transitioning the original MiSeq to end-of-life service. By upgrading to the new MiSeq i100, the CQLS will replicate our current sequencing abilities while drastically reducing instrument maintenance costs for the CQLS and consumable costs for OSU researchers.

The Illumina MiSeq i100 is a next-generation sequencer that sequences low-volume flow cells, 5 Million sequences in 300 or 600 base-pair lengths or 25 Million sequences in 100, 300, or 600 base-pair lengths. The MiSeq i100 is quicker and cheaper to run than other short-read sequencers.

Key features include:

  • Cost efficiency: Cost-effective consumables enable more affordable sequencing
  • Speed: Dramatic reduction in run times: as fast as four hours, with same-day results (4× faster than MiSeq)
  • Room-temperature shipping and storage for reagents: Allowing for greater flexibility to sequence on demand without the need to thaw reagents
  • Simplicity: Simpler, streamlined operations for various levels of sequencing experience

The new MiSeq i100 is upgraded from the original MiSeq in several ways.  Flow cells are lower-cost and higher volume so researchers will be able to obtain more sequence at a lower price. The small volume sequencing (1M) of the original MiSeq is no longer offered but researchers will be able to sequence higher volume runs at a lower or similar price.  Running the instrument is also more streamlined: run times are 4x faster; many reagents and consumables are now stored in room temperature; the instrument is simpler to maintain resulting in a lower yearly service contract price.

MiSeq i100 overview:

https://www.illumina.com/systems/sequencing-platforms/miseq-i100.html

MiSeq i100 specification:

https://www.illumina.com/systems/sequencing-platforms/miseq-i100/specifications.html

MiSeq i100 research applications:

https://www.illumina.com/systems/sequencing-platforms/miseq-i100/applications.html

Interview: Pacific Biosciences (PacBio) Sequel Service

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Aaron Trippe discusses the changes and challenges of working with the PacBio Sequel since 2016. He discusses improvements in the technology since 2016 and has advice for user who would like to utilize this service.

Aaron Trippe, our long-time PacBio technician, stands next to the CGRB’s Pacific Biosciences Sequel.

Q1: How long have you been running the PacBio sequencing service at the CGRB?

The CGRB was one of the early adopters of the Sequel, the second phase of long read genomic sequencing technology from Pacific Biosciences.  It arrived here on campus in August of 2016.  Since then the technology has made significant improvements to the user-interface, and has tremendously increased read lengths and output. 

Q2: You started up the PacBio sequencing service at the CGRB. What has been the most challenging aspect about developing this service?

Aside from the continually changing and evolving technology, one of the most challenging aspects of the service is getting everything you feed the machine to produce optimal results.  One of the advantages of the technology is that you are sequencing native DNA, but that also makes it challenging when working with an organism that traditionally is difficult to work with and considered problematic.  Finding ways to produce super clean and high molecular weight DNA from just about everything is probably the largest hurdle to working with the technology as a service provider.  The keys to success are definitely within the sample quality.  Having pure, high molecular weight DNA is essential to take advantage of the long read aspect of the technology, and is directly correlated to the quality of the sequencing output.

Q3: What type(s) of project(s) would you recommend to use PacBio’s long read technology?

The technology is great for just about any sequencing application.  With the long reads, you have access to regions of DNA that were not previously accessible due to repetitive regions in genomic DNA.  There is enough output to multiplex several microbial genomes on a single SMRT Cell.  Complete sequences of multiplexed amplicons using Circular Consensus Sequencing for high fidelity reads of shorter inserts. With the read lengths exceeding that of RNA transcripts, Isoform sequencing using the Iso-seq application is also available for obtaining complete transcripts.

Q4: Favorite or most interesting project you’ve worked on?

Since managing the PacBio Sequel, I’ve gotten to work with plants, animals (vertebrates/invertebrates), fungi, bacteria, and insects for the local scientific community, and beyond.  I can’t say that I have had a favorite organism, and they have all been interesting projects, but overcoming challenges with successful results always feels rewarding.

For more information please visit the CGRB website: https://cgrb.oregonstate.edu/core/pacbio

Note: We wish Aaron the best as he purses a new opportunity and are grateful he was able to develop a successful PacBio Service at the CGRB! For future sequencing inquires please contact Katie Carter.

Close up of a PacBio SMRT cell.