DNA Sequencing Core Facility

The DNA Sequencing Core Facility provides DNA sequencing services to investigators at CMMT and CFRI, as well as off site researchers. It is equipped with the ABI Prism 3130xl Genetic Analyzer, a 16-capillary fluorescence-based DNA analysis system.

In addition to DNA sequencing, the 3130xl system supports a variety of applications including comparative sequencing, DNA fragment analysis, and genotyping. Skilled staff members are ready to lend their expertise in sequencing PCR products, plasmids, and BACs with a turn-around time of 1 to 3 days.

Since 2002, the facility has run over 96,000 analyses of samples for over 165 research groups at the CMMT, BCCH, UBC, SFU, UVic, and numerous hospital, industry and government research groups.

DNA SEQUENCING

Sequencing is performed on an ABI 3130xl 16-capillary automated genetic analyzer. Samples are typically run on a 50 cm capillary yielding 800 to 900 bp with results typically available in one to three business days. 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 V1.1 and dRhodamines) are utilized as required for difficult to sequence templates.

Sequence data is provided electronically as analyzed ABI files (.ab1), though are available in other formats (see Protocol Notes).

CUSTOM DNA OLIGO SYNTHESIS

Custom DNA oligo synthesis is now available through the IDT – CMMT Stores Web-Portal. For information on this portal, please visit the CMMT/CFRI Stores webpage. To go directly to the portal click here: IDT – CMMT Stores Portal.

SAMPLE PREPARATION—STANDARD SERVICE

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)
  • Samples must be normalized to the same concentration with the following minimum quantities and concentration ranges:
Sample typeMinimum quantityConcentration range
Plasmid30 to 100 ng/ul
<7 kb160 ng
7-8 kb170 ng
9-10 kb180-200 ng
11-15 kb200-300 ng
BAC1000 ng100 to 1000 ng/ul
PCR Products10 to 20 ng/ul
100-200 bp10-15 ng
300-500 bp20-30 ng
600-800 bp35-45 ng
1,000-2,000 bp60-80 ng
  • The actual concentration of each sample must be provided.
  • There is a $3/reaction surcharge if samples must be adjusted to normalize the concentrations to the same concentration within the required range.
  • Re-suspend template and primers in dH2O or 10mM Tris pH8.0 to 8.5, no TE.
  • Standard primers are provided (see Primers). Alternatively, please provide non-standard primers at 3.2pmol/ul.
  • If submitting more that 7 samples with the same primer sets, please submit samples in 8-strip PCR tubes or 96-well plates.
  • Discounted pricing available if primers are pre-mixed and all samples are standardized to the same concentration, within the ranges specified above, and provided in a 96-well plate or 8-strip PCR tubes (see below).

PRE-MIXED SAMPLES SERVICE

A more economical DNA sequencing option is available for plasmids and PCR products. The Pre-Mixed Samples Service special pricing is available if the following sample submissions requirements are followed:

  • Primers must be pre-mixed with your plasmid or PCR product samples.
  • Samples must be submitted in 8-strip PCR tubes or 96-well plates.
  • Primer concentration, total sample volume, and sample concentration must meet the following specifications:
Sample typeDNA Length (including vector)DNA Amount (ng)Primer Amount (pmol)Total Volume (ul)
Plasmids< 6kb3001015
6-10kb4001015
>10kb5001015
PCR Products<1000bp10ng per 100bp1015
1kb to 2kb80ng to 120ng1015

READY-TO-RUN SERVICE

Please provide the facility with your cycle sequenced and purified sequencing products (in 8-strip PCR tubes or 96-well plates if more than 6 samples). 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.

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.

FEES AND INVOICING

DNA sequencing pricing for Academic researchers. Private sector pricing is available upon request.

Samples submitted< 1616 to 47>47
Prepared by facility
Standard service
(Normalized concentration)
$12.50$10.50$8.50
  Surcharge to Normalize
  Sample Concentration
$3.00$3.00$3.00
Pre-mixed Samples
(Normalized Concecntration,
8-strip tubes or 96-well plates)
$10.50$8.50$7.50
Ready-to-run$4.25$3.75$3.75

The following DNA sequencing pricing applies to CMMT and CFRI Academic researchers.
Samples submitted< 1616 to 47>47
Prepared by facility
Standard service
(Normalized concentration)
$11.50$9.50$7.50
  Surcharge to Normalize
  Sample Concentration
$3.00$3.00$3.00
Pre-mixed Samples
(Normalized Concecntration,
8-strip tubes or 96-well plates)
$9.50$7.50$6.50
Ready-to-run$3.75$3.00$3.00

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). See Sample Preparation – Standard Service above for more information.
  • To be eligible for our “Pre-Mixed Samples” pricing, samples mixed with primers submitted must conform to requirements detailed in the Pre-Mixed Samples Service section above.
  • 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 8-strip PCR tubes or 96-well plates if greater than 6 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. HST is applicable to all invoices unless paid by UBC Journal Voucher.

GENOTYPING SERVICES

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.

SAMPLE SUBMISSION

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 BCCHR shipping and receiving at 950 West 28th Avenue (before 4:00 pm), by calling 604-875-3814 to reach the facility, or by courier to the address below. On site researchers may drop off samples in the facility’s freezer in room 3028.

CONTACT INFORMATION

For additional information and to submit samples please contact:

Ms. Liz Hui
(604) 875-3814
dna@cmmt.ubc.ca

Mailing Address:

CMMT/BCCHR DNA Sequencing Core Facility
Attention: Ms. Liz Hui
The Centre for Molecular Medicine and Therapeutics
950 West 28th Avenue, Room A3-193
Vancouver, BC
V5Z 4H4 Canada

For further information on CMMT Core Facilities, please contact:

Michael Hockertz
hockertz@cmmt.ubc.ca
(604) 875-3816