DNA Sequencing Core Facility

 

The DNA Sequencing Core Facility provides Sanger DNA sequencing services to investigators at CMMT, BCCHR, and off-site researchers. It is equipped with the ABI Prism 3500xl Genetic Analyzer, a 24-capillary fluorescence-based DNA analysis system.

In addition to DNA sequencing, the 3500xl 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 1 to 3 day turn-around time.

Since 2002, the facility has run over 325,000 analyses of samples for over 215 research groups at the CMMT, BCCHRI, UBC, SFU, UVic, and numerous hospital, industry and government research groups.

CMMT DNA Sequencing Core to Remain Open During COVID-19 Research Curtailment

To meet the research requirements of customers engaged in COVID-19 research and those who have returned to work, the CMMT DNA Sequencing Core Facility will continue to operate during the research curtailment implemented at UBC. Please submit your samples as usual.

DNA SEQUENCING

Sequencing is performed on an ABI 3500xl 24-capillary automated genetic analyzer. Samples are run on a 50 cm capillary which can yield up to 800 to 900 bp, with results typically available in one to three business days. We offer both Full Service sequencing of your DNA templates and 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 utilizing the ABI BigDye v3.1 Terminator chemistry.

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

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)
  • Normalize samples to the same concentration with the following minimum quantities and concentration ranges:
Sample Type

Minimum Quantity
required per reaction

Minimum Quantity
required for submission
Concentration Range1
Plasmid      
<7 kb 160 ng 320 ng 25-160 ng/ul
7-8 kb 170 ng 340 ng 26-170 ng/ul
9-10 kb 180-200 ng 360-400 ng 30-200 ng/ul
11-15 kb 200-300 ng 400-600 ng 46-300 ng/ul
PCR Products      
100-200 bp 10-15 ng 20-30 ng 2.3-15 ng/ul
300-500 bp 20-30 ng 40-60 ng 4.6-30 ng/ul
600-800 bp 35-45 ng 70-90 ng 6.9-45 ng/ul
1000-2000 bp 60-80 ng 120-160 ng 12.3-80 ng/ul
  1. If the concentration is significantly below the minimum concentration it can be set up with increased sample and reagent volumes.
  • The concentration of each sample must be provided.
  • There is a $3/reaction surcharge if the sample concentrations must be adjusted to the same concentration or within the required range.
  • There is a $1.50/reaction surcharge for specialty sequencing (BAC or cosmid) and for samples with low concentration to cover the greater cost of sequencing reagents.
  • Re-suspend template and primers in dH2O or 10mM Tris pH8.0 to 8.5 (cannot be resuspended in TE).
  • Standard primers) are provided. 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 (see below).

PRE-MIXED SAMPLES SERVICE

Pre-Mixed Samples Service special pricing is available for plasmid and PCR products if the following 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 (our sample submission excel file now includes a convenient pre-mix calculator):
Sample type DNA Length (including vector) DNA Amount (ng) Primer Amount (pmol) Total Volume (ul)
Plasmids < 6kb 300 10 15
  6-10kb 400 10 15
  >10kb 500 10 15
PCR Products 100-200 bp 20-30 10 15
  300-500 bp 40-60 10 15
  600-800 bp 70-90 10 15
  1kb to 2kb 120-160 10 15

READY-TO-RUN SERVICE

Please provide the facility with your cycle sequenced and purified sequencing products (if more than 6 samples in 8-strip PCR tubes or 96-well plates). The facility will run your samples, confirm sequencing results, and provide results in ABI .ab1, or your preferred electronic format.

See our protocol notes page for further information on the ABI 3500xl Genetic Analyzer, DNA template preparation, sequencing reaction protocol, and analysis of results—including links to free analysis software.

FEES


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

Samples submitted < 16 16 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 Concentration,
8-strip tubes or 96-well plates)
$10.50 $8.50 $7.50
Surcharge for BAC/cosmid
or low concentration samples
$1.50 $1.50 $1.50
Ready-to-run $4.25 $3.75 $3.75

The following DNA sequencing pricing applies to CMMT and BCCHR Academic researchers.

Samples submitted < 16 16 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 Concentration,
8-strip tubes or 96-well plates)
$9.50 $7.50 $6.50
Surcharge for BAC/cosmid
or low concentration samples
$1.50 $1.50 $1.50
Ready-to-run $3.25 $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.
  • Specialty sequencing (BAC, cosmid) and other samples that require additional sequencing reagents (ie. concentration is outside of indicated range) will incur a $1.50/reaction surcharge.
  • 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.

GENOTYPING SERVICES

DNA fragment analysis is performed on the ABI Prism 3500xl 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 DNA sequencing request form that can either be printed or sent as an email attachment.

Samples can be 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.

BILLING AUTHORIZATION AND INVOICING

Invoicing will be processed on a monthly basis by the Workday Internal Service Delivery (ISD) process for UBC customers.  To enable monthly billing to your UBC grant, please complete the ISD Authorization Form available here. Non-UBC customers will be invoiced monthly.

CUSTOM DNA OLIGO SYNTHESIS

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

CONTACT INFORMATION

For additional information and to submit samples please contact:

Ms. Aida Sobhani
(604) 875-3814
dna@cmmt.ubc.ca

Mailing Address:

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

Dropping Off Samples in Person?

Please meet us at the south entrance of the BC Children’s Hospital Research Institute. This is Entrance #4 shown on the map on the Contact Us page.

For further information on CMMT Core Facilities, please contact:

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