A leading contributor of science and knowledge through discoveries.

 

Services

Next Generation Sequencing Platform
523-715 McDermot Avenue
Winnipeg, MB
R3E 3P4

Contact: Dr. Deborah Tsuyuki
email: dtsuyuki@chrim.ca

The NGS platform was established by Dr. Jim Davie as a University of Manitoba facility for next generation sequencing. The NGS platform has been established and supported by Canadian Foundation for Innovation (CFI), Manitoba Research and Innovation Fund (MRIF), University of Manitoba Faculty of Medicine, Cancercare Mb, Manitoba Institute of Child Health (MICH) and Manitoba Institute of Cell Biology (MICB).

The platform’s original emphasis was on epigenetic research (ChIP Seq and Methyl Seq), but is available to all University of Manitoba and MICH researchers for many other applications (transcriptomes, exomes, small RNA, microbial genomes). For estimated costs, please see instrument pages. These costs include all standard NGS reagents and consumables, but not non-standard consumables, such as FFPE nucleic isolation kits. Please consult us for a quote specific to your project.

We have two cutting edge sequencers and all the ancillary equipment required for library preparation and the critical quality control of nucleic acid input. Our sequencers are:

Each machine has a different chemistry and provides different read lengths, so for the best instrument for your project, please consult the table below

Instrument Capacity Maximum read lengths Applications
Ion Torrent PGM 10 Mb (314 chip), 100 Mb (316 chip), 1 Gb (318 chip) 400 bp reads Microbial sequencing, targeted resequencing, amplicon resequencing, small RNA sequencing

 

Illumina MiSeq 15 Gb 300 bp, paired end

 

Targeted resequencing, 16S metagenomics, amplicon resequencing, small RNA sequencing

The platform currently has 3 employees, Dr. Deborah Tsuyuki (manager), Mr. Aleksander Ilic (assistant manager) and Dr. Wayne Xu (bioinformatician).

We plan to organize seminars and workshops throughout the year on Next Generation Sequencing and Bioinformatics. We will also invite companies such as Illumina and Life Technologies to present information seminars as new technologies and upgrades become available. Please keep an eye on our seminar page from time to time for updates. If you would like to have a seminar on NGS or bioinformatics for your department, please contact us.

If you want to initiate a Next Generation Sequencing project, but do not see information for your particular application on these pages, please do not hesitate to contact us.

Additionally, we have three instruments that are useful for sample preparation.

  • The Agilent 2100 Bioanalyzer is used for visualization of RNA and DNA. There are several run types available for DNA, including the DNA 1000 (35bp – 1.0 Kb) and the High Sensitivity (35 bp – 10.3 Kb). The RNA pico run allows for RIN (RNA integrity number assessment).
  • The Covaris S220 ultra focused sonicator is used for controlled shearing of cells and DNA for ChIP Seq and library building.
  • The Invitrogen Qubit 2.0 is a fluorometric nucleic acid quantitation instrument and is particularly vital for low input samples.

NEW! In addition, we offer most library preparation services. If you wish to outsource your NGS needs, building the library in house allows much more QC than is possible with a total outsourced project. In addition, most large platforms can perform NGS on libraries with a faster turn-around than with nucleic acid samples.

  1. We will QC your samples to determine their quality to move forward. If they are inadequate in any way, we will let you know and you have the option of preparing new samples.
  2. We will ask you to perform a qPCR against a known positive control to confirm enrichment of at least one gene (preferably two) between the control and treatment sample.
  3. We will build your library and make an aliquot available for a confirmatory qPCR to make sure that enrichment has been maintained. If there is no enrichment, we will let you know and you have the option to stop and prepare more samples.

The library preparation is critical to the success of NGS and is the second leading cause of failure (the first cause is inadequate sample). With the library prep done in house, you have the ability to control the libraries that go forward and incur the majority of cost involved in NGS.

NGS-Illumina-MiSeq-150x106 Illumina MiSeq costs

 

NGS-Ion-Torrent-PGM-150x106 Cost-of-Ion-Torrent