DNA Sequencing Facility

The Centre for Genomics and Proteomics, DNA Sequencing Facility offers sequencing and genotyping services that are fast and reliable. All samples are processed on an Applied Biosystems 3130xl Genetic Analyzer.

DNA Sequencing Service

All sequencing reactions at the Facility are carried out using Applied Biosystems BigDye version 3.1 terminator chemistry on Applied Biosystems 9700 Gold Block thermal cyclers. Cleanup of dye terminators uses CleanSeq magnetic bead technology.

The Facility supplies SP6, T7, T3, -21M13, M13 Rev primers free of charge. Please check the form below for their correct sequence and check that this aligns with your template.

Please supply any other primers that you require at the correct concentration (see table below).

Primer Sequences pdf document

Current Charges

The current charges for our sequencing services are as follows (minus GST):

  • Facility reactions (for external customers) - $27.00
    Please supply in 1.5ml tubes. Facility does the fluorescent chemical reaction & electrophoresis.
  • Facility reactions (for The University of Auckland) - $20.00
    Please supply in 1.5ml tubes. Facility does the fluorescent chemical reaction & electrophoresis.
  • Own reactions (for all customers) -  $10.00
    Please supply in 1.5ml tubes as a dried pellet. You do the fluorescent chemical reaction, Facility does the electrophoresis.
  • Bulk reactions (for all customers) - $5.00
    Please supply in 96 well format, in lots of 16. You do the fluorescent chemical reaction, Facility does the electrophoresis.


The templates and primers need to be supplied as follows in 1.5 ml tubes or 96 well format and clearly labelled:

Concentration and Volume requirements Plasmid M13  PCR Product
Template concentration – in water only if possible 200ng/µl 100ng/µl 5ng/ul - 20ng/µl require 2.5ng/100bp
if<1kb require 5ng/100bp
if >1kb
Volume template 5µl 5µl 5ul if <1kb,
10ul if >1kb
Primer concentration – in water only if possible 5pmol/µl 1pmol/µl 5pmol/µl
Volume primer 5µl 5µl 5µl

Your own and bulk reactions should be supplied in a dried form after the sequencing cleanup. Bulk reactions must be supplied in an Applied Biosystems 96 well place, catalogue number, N8010560 or equivalent.

Genotyping Service

Genotyping automates DNA fragment analysis using internal-land standards. The internal-land standards permit accurate and precise base calling and eliminates bandshift artifacts and run-to-run variation. It can size PCR products (STR’s, VNTR’s and RAPDs) and accurately analyse molecular lengths in the 50-1000 nudeotide size range.

Provide 1-2ul final volume or a dried pellet for singleplex/multiplex samples in 96 well plate format. The Facility provides the ladder.

Options:

  1. Rox (RED) ladder 400HD / 500HD
    For 6 fam/hex/ned combination.
  2. Liz (ORANGE) ladder 600 /1200
    For 6 fam/vic/ned/pet combination.

The current charge is $5.00 per sample (minus GST).

To make a request for one or more of these services, please download the appropriate pdf request form and send together with your samples:


1. Form A CGP Sequencing request

2. Form B CGP Electro request

3. Form C CGP Bulk Electro request

4. Form D CGP Genotyping request

5. Form E CGP 7900 request

6. Form F CGP Bioanalyzer request


For a list of free software packages available for viewing sequencing and genotyping data download the pdf document.

Reference guides from Applied Biosystems:

1. Applied Biosystems Sequence pdf guide

2. Applied Biosystems Genescan pdf guide

For further information visit the Applied Biosystems website found below:

Applied Biosystems (http://www.appliedbiosystems.com.au/)


Contact details:

Kristine Boxen
Centre for Genomics & Proteomics
DNA Sequencing Facility
School of Biological Sciences
The University of Auckland
Private Bag 92019
Auckland

Physical Location
3A Symonds St
Thomas Building 110
Room 212

Phone: +64 9 373 7599 ext 87293
Fax: +64 9 373 7417
Email: k.boxen@auckland.ac.nz


Other Services

A number of additional machines are located in the Thomas Building, Room 212, DNA Sequencing Facility.

Agilent Bioanalyzer 2100

The Agilent Bioanalyzer 2100 is used to determine the quality and quantity of RNA/DNA samples. Twelve samples are loaded onto one chip and run on the machine via electrophoresis. Customers can book the machine and run their own samples. The current charge per run is $5.00. It costs $43.00 for one nanochip with reagents and run.

Applied Biosystems 7900HT Sequence Detection System

The Facility has one machine that can be booked and used by customers. It holds one 384 well tray per run. Customers can book the machine and run their own samples. The current charge per run is $40.00

Applied Biosystems 9700 Thermal Cycler Gold Block

The Facility has six machines that can be booked and used by customers. They are 96 well tray format. There is no charge for this service.

Nanodrop Spectrophometers

The Nanodrop is a low volume spectrophotometer that does not require a curvette. It can be used to measure the quantity of RNA/DNA and protein. It only requires 1µl of your product. The Facility has two machines that are one well and one machine that has eight wells. There is no charge for this service.

Applied Biosystems 3130XL Genetic Analyzer

The Facility has one 3130XL machine that has 16 capillaries. It uses capillary electrophoresis to separate the fragments and can be used for sequencing and genotyping applications. The Facility runs this machine and prices vary depending on the application.

Corbett 384 well PCR machines

The Facility has two machines. There is no charge for this service.

Computer Software

The Centre for Genomics and Proteomics has a Dell Optiplex GX270 computer available with software programmes to analyse your data. It operates via a booking system.

The programmes available are:

  • Genescan Analysis version 3.7
  • Genotyper version 3.7
  • Genemapper version 4
  • Seqscape version 2.1.1
  • Vector NTI Advance 9.0
  • Primer Express v2.0
  • qBase


A number of liquid handling robots are available to customers free of charge and are located in the Thomas Building, Room 207, the Robotics room. The Facility supplies tips for use on the robots that are available at cost.

Eppendorf epMotion 5075
Beckman Biomek 3000
Beckman Biomek 2000



For sequencing, genotyping and real time PCR applications contact:


For Agilent Bioanalyzer 2100 applications contact:


For any further problems or questions contact Kristine Boxen: