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DNA-sequence

Waikato DNA Sequencing Facility (WDSF)

Sequencing Services

Each DNA template that meets the requirements for sequencing is reacted using a commercial dye terminator chemistry and a specified single primer per reaction, including several common primers the WDSF provides free of charge or using any custom primer suitable for sequencing. DNA sequences are then resolved using an ABI 3130XL fitted with 50 cm capillary arrays. Resulting trace and sequence information is then made available according to individual customer requirements.

  • Dye Terminator Chemistries
    Sequencing reactions are performed using Applied Biosystems Big Dye v3.1.
  • Primers
    Sequencing requires only a single primer for each reaction. The sequencing reaction has linear reaction kinetics due to this single primer, rather than exponential PCR reaction kinetics.  Residual primers or DNA fragments which could initiate DNA replication can often cause trouble and we advise that all practicable steps are taken to ensure template and primer purity.

Genotyping Services

The Waikato DNA sequencing facility operates a Genotyping service based on the 3130 Genetic Analyser and GeneMapper 4 series software. The DNA template requirements for genotyping match those of the sequencing service in terms of required concentrations and template purity. Genotyping requires one primer from each pair to be labelled with a suitable reporter.

  • Genotyping Ranges
    The fragment profiling system is capable of accurately differentiating genotypic fragments up to 1200bp in length in two distinct ranges according to the standard. The WDSF can supply standards for 600 or 1200 bp runs.
  • Fluorescent Reporters
    Each primer pair requires that one primer of the pair is labelled with a fluorescent reporter, the availability of certain reporters may depend on your chosen primer supplier. The WDSF can accept and utilises the following reporters.
  • Results
    Results are available as either a Fragment List (listing of all fragments) or a called List with results sorted and counted (binned) according to customer specified product lengths.
  • Availability
    Due to the array nature of the genotyping service, we prefer to run at least 16 samples at a time.

Ion Torrent PGM Services

Detect variants with targeted gene sequencing against amplicons, type bacteria or viruses, and characterise novel microbes. Capable of producing millions of reads up to 500bp the PGM lets you create detailed metagenomic diversity profiles and complete de novo sequencing projects.


Results

We will notify you via email when your sequencing request is completed. Results can be made available in a number of ways, as listed below. Please indicate your preference(s) by ticking the appropriate box(es) on the request form.

Email
The sequence text file is sent via email in FASTA format.

Electropherogram printout
The electropherograms are sent as a hard copy via the mail.

File Transfer Protocol (FTP)
This method allows you have access to both the text and sequence files from our secure FTP server. Researchers are able to edit their trace data and perform downstream analysis. Please contact us if you wish to be able to access your results this way. We will provide instructions to download your results to your computer using FTP software or via a Browser.

Archiving

All templates and primers are stored frozen for at least three months and resulting data is securely archived, so should you experience a data loss, need electronic versions of your results, or find that the return of your research material would be beneficial, please contact us.

Template Archives
All supplied templates and primers are stored frozen (-20°C) for a minimum period of three months and can be called upon for any new reactions or any remainder returned upon request.

Results Archives
All resulting data is archived where possible, should you experience a data loss, or find that the electronic versions of any present or past result would now be beneficial, we can make this available to you from our archives.


Fast Turnaround Time

We endeavour to return your sequencing results the next business day following receipt. However, the turnaround time can be as high as 3 working days depending on service demand.

If you have samples of an urgent nature, please let us know so we can do our best to accommodate your requests within your demanding time schedule.

International Service

The WDSF is pleased to again accept international samples following the reclassification of DNA products (purified non-vector material) under section 7.6 (1) (g) of the Ministry for Primary Industries biological products classifications. If your research group is outside of New Zealand, please contact us regarding your samples and the necessary declarations for customs purposes before shipping.


Sample requirements

Find out what is required when submitting a sample for processing.

Costs

For the latest equipment and analytical costs for external clients, please refer to the Science & Engineering Services Fees Schedule.

Tips & Troubleshooting

Discover our template tips, find solutions to common problems in template preparation and read our disclaimer.