DNA Sequencing Core Facility

Sequencing is performed on an ABI 3130xl 16-capillary automated genetic analyzer with a capacity of approximately 192 samples sequenced in 24 hours (see protocol notes). Samples are typically run on a 50 cm capillary yielding 800 to 900 bp. We offer both Full Service sequencing of your DNA templates, or a Ready-to-Run service if you prefer to do your own sequencing reactions.

We sequence single or double stranded DNA from plasmids, PCR products, BAC, PAC and cosmid templates as well as sequencing of bisulfite converted methylated DNA utilizing the ABI BigDye v3.1 Terminator chemistry. Alternate chemistries (ABI BigDye dGTP and dRhodamies) are utilized as required for difficult to sequence templates.

Sequence data is generally provided electronically as analyzed ABI files (.ab1), though are available in other formats (see protocol notes), or optionally as printed chromatograms.

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As successful sequencing reactions are highly dependent on the quality and accurate quantitation of templates provided, please adhere to the following points for all samples submitted:

• Purify templates using commercially available nucleic acid purification kits (see protocol notes for recommendations)

• Provide samples with the following minimum quantities and concentration ranges:

  Sample type	Minimum quantity	Concentration range
  Plasmid	300 ng	30 to 100 ng/ul
  BAC, PAC, or Cosmid	600 ng	100 to 1,000 ng/ul
  PCR Products		10 to 20 ng/ul
  100 bp	5 ng
  500 bp	20 ng
  1,000 bp	35 ng
  2,000 bp	60 ng

   

• The actual concentration of each sample must be provided.

• Discounted pricing available for submissions of more than 16 samples if all are standardized to the same concentration, within the ranges specified above, and provided in a 96-well plate (see fees & invoicing below).

• For PCR Products, provide a gel electrophoresis picture with notation of volumes loaded on gel and, if possible, a DNA Quantitative Marker loaded as well (i.e. Invitrogen Low DNA Mass Ladder, Cat. No. 10068-013).

• Re-suspend template and primers in dH₂O or 10mM Tris pH8.0 to 8.5, no TE or EDTA.

• Standard primers are provided (see primers). Alternatively, please provide non-standard primers at 3.2pmol/ul.

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Please provide the facility with your cycle sequenced and purified sequencing products. The facility will run your samples, confirm sequencing results, and provide results in ABI .ab1, or your preferred electronic format. See our protocol notes for details.

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See our protocol notes page for further information on the ABI 3130xl Genetic Analyzer, DNA template preparation, sequencing reaction protocol, and analysis of results—including links to free analysis software.

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DNA sequencing pricing for Academic researchers, effective July 1st, 2009. Private sector pricing is available upon request.

The following DNA sequencing pricing applies to CMMT and CFRI Academic researchers and members of the CGDN.

Additional information on fees:

• All fees are quoted in Canadian dollars and are subject to change. Please contact the facility for the most up-to-date information on fees and availability.

• To be eligible for volume discounts (more than 15 samples), all samples must be of same type and submitted at the same time.

• "Standard service" includes reaction setup, sequencing reaction, and provision of analyzed .ab1 files (or other format upon request).

• To be eligible for our "normalized concentration in 96 well plates service", samples must be of same type, standardized to the same concentration (within the ranges specified in the above concentration range table), and provided in 96-well format plates.

• For "ready-to-run", the user provides cleaned sequencing products, facility denatures and runs samples on sequencer, and provides analyzed .ab1 files (or other format upon request). Please provide samples in 96-well plates if greater than 16 samples submitted. Please contact facility for further details.

• If a sequence fails due to facility's error or equipment malfunction, it will be repeated at no charge. All other sequence failures and repeats are customer's responsibility.

Invoicing will be processed on a monthly basis by Journal Voucher for UBC customers and by invoice for non-UBC customers. Payment should be made upon receipt of invoice. GST is applicable to all invoices unless paid by UBC Journal Voucher.

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DNA fragment analysis is performed on the ABI Prism 3130xl Analyzer. Our facility can analyze fragments from 50-1000bp in size from AFLP, and microsatellite markers (see protocol notes). Size standards are provided by the facility. Please contact us for further details and for pricing for your project.

Additional genotyping and gene expression profiling services based on the Illumina BeadStation 500GX system are available from the CMMT genotyping and gene expression core facility.

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Click here to download the sequencing request form that can either be printed or sent as an email attachment. If your browser displays the Excel file, then you can print directly from your browser, or choose 'File > Save As' to save the file to your disk.

Samples can dropped off at the CFRI shipping and receiving at 950 West 28th Avenue (before 4:00 pm), by calling extension 3814 on the Oak Street entrance intercom, or by courier to the address below. On site researchers may drop off samples in the facility's freezer in room 3028.

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