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Instrumentation

The Genomics facility operates the following sequencing instrumentation:

Illumina NextSeq 500 sequencer. These desktop sequencers can be operated in high-throughput mode with 400 million read sequencing cartridges for either 1x75 bp, 2x75 bp, or 2x150 bp sequencing to generate up to 30, 60, or 120 Gigabases of sequence, respectively.  This is our preferred platforms for large genome, exome, or gene expression (transcriptome) projects. Sequencing runs take only 1-2 days to perform and each instrument can produce 6-12 Terabases of sequence annually. Two NextSeq 500 instruments are available for our use. One is in our sequencing instrumentation suite (HSC B104A) and the second NextSeq is in the nearby ACWA microbiology laboratory.

  • Illumina MiSeq sequencer. The MiSeq desktop sequencer is Illumina’s smallest capacity sequencer with v3 chemistry kits supporting 25 million reads with either 1x150 bp, 2x75 bp, or 2 x 300 bp sequencing to generate ~ 15-30 Gigabases of sequence. Version 2 MiSeq chemistry kits in six other sizes are also still available. This is the preferred platform for low diversity PCR amplicons, i.e. 16 S rRNA metagenomics, and small genome sequencing. Sequencing takes between 1-3 days to run. One MiSeq is located at our Alberta Children’s Hospital site within the Molecular Diagnostic Laboratory and a second MiSeq in the Nicole Perkins Microbial Communities Core Labs is operated by the Snyder Institute for Chronic Diseases (contact Karen Poon). We can also perform library preparations for any of the other MiSeq instruments at the university.
  • Ion Torrent Personal Genome Machine (PGM). The PGM sequencer uses novel pH sensing semiconductor sequencing chips for rapid 200 bp or 400 bp sequencing. Three semiconductor chips are available with read capacities between ~ 0.5-5 million reads which can produce up to ~ 1 Gigabase of sequence. This is the preferred platform for sequencing Ampliseq gene panels, PCR amplicons, and small genomes. A PGM run takes requires only 2-4 hours of sequencing, but total run preparation time is about 2 days. Our PGM sequencer is used for clinical diagnostics within the Alberta Children’s Hospital, but it is also available for basic research projects.
  • Oxford Nanopore Technologies MinION. Our facility is participating in the MinION Access Program (MAP) to help develop single-molecule nanopore-based DNA sequencing. We have both an original (classic) MinION device and the recently released MinION Mk1 device. These devices use disposable cartridges with about 500 nanopore sensors. Sequencing is extremely fast (30-100 bases/sec) and read lengths are only limited by the length of the DNA fragments (typically up to ~ 60,000 bp). Please contact us if you have a project which might benefit from this powerful, but still evolving, technology.

The Genomics facility also has extensive equipment for library preparations, including:

  • Nanodrop UV/Vis spectrophotometer for UV quantitation of nucleic acids samples. These spectrophotometers are used for low volume quantitation of microgram quantities of DNA or RNA and to assess A260/A280 and A260/A230 ratios. However, these instruments can overestimate the amount of material present when low concentrations are being measured and so Nanodrop measurements are not recommended for next-gen sequencing library quantitation. Instead, quantitation on a Qubit fluorimeter using either the DNA or RNA specific assays is required.
  • Agilent 2200 TapeStation for quantitation, fragment length, and quality (i.e. RIN scores) measurement using genomic DNA, DNA, and RNA assays.
  • Sage Pippen Prep for automated and targeted size selection (90 bp – 1.5 kb) of DNA fragments on pre-cast agarose gel cassettes.
  • Covaris sonicators (S2 and S220 models) for controlled shearing of DNA samples using Adaptive Focused Acoustics (AFA).

To minimize sample cross-contamination, all next-generation sequencing libraries are performed in a separate laboratory suite located away from the next-gen sequencing instruments. This suite is in the former Libin Gene Therapy suite in the basement of the Heritage Medical Research Building (HMRB B020A-D). The suite contains two air-locked isolated laboratories which are used for sample intake and pre-PCR reaction set-up. A third laboratory contains our RNase-free and post-PCR work areas.