Some of our frequently asked questions – select a question to reveal the answer.
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DNA and samples requirements | Back to top
For DArTseq, but also for DArTseqLD and DArTcap, the DNA needs to be suitable for digestion by restriction enzymes and ligation to adaptors.
DArTag and DArTmp are less affected by some impurities as we do not use Restriction Enzymes in those technologies, but good quality DNA is always the best assurance of good outcome of the service.
Obtaining higher purity DNA has the following long term advantages:
- Improved shipping endurance;
- Improved storage duration;
- Higher data quality and volume; and
- Broader usage over multiple tests and assays, over a longer time period.
In the last 17 years we processed samples extracted with a very broad range of methods, both “in-house” procedures, predominantly CTAB-based, and a large diversity of commercial extraction kits.
Yes, many of our clients use our DNA extraction service, predominantly those from Australia as shipping of samples within the country does not have any restrictions. When our international clients experience difficulties with obtaining good quality DNA we usually find a way to bring those samples in using one of our many Import Permits. Please inquire about your specific case and we will provide recommendations.
We recommend using the following protocol prior to sending the samples to us. This will help you receive the best quality data for your samples in less time, preventing you from having to resend those samples of poor quality if any.
DNA quality of the samples is controlled by:
- Incubating 1µl of DNA in Restriction Enzyme buffer at 37°C for 2 hours.
- Resolve the DNA on a 0.8% agarose gel in 1x TAE buffer.
- Inspect the gel image for your samples. Good quality DNA gives a high molecular weight band on the gel image.
This protocol is a mock digest to detect the presence of buffer-activated (usually Mg dependent) nucleases: no restriction enzyme is used.
Another option for you is to send us the image of the DNA quality control you already have, for us to ensure the DNA is of sufficient quality for DArT genotyping.
To perform a DArT assay, we require you to send us about 20µl of an aqueous solution of DNA at 50 to 100 ng per µl, not more. Excessive concentration is detrimental to the assay. If your DNA is concentrated please dilute it.
The assay itself uses 2µl of recommended concentration DNA, however we require a larger volume to reduce problems during shipment and to be able to perform Quality Control/Method Test (for new organisms).
We were able to process samples with much lower DNA concentration than recommended, including DNA extracted from museum and herbarium specimens often over 100 years old, but the best data quality is assured by providing samples in recommended range. Our assays generally tolerate up to 3-4 fold variation in DNA concentration within a plate.
Please contact us if you have any questions regarding the quality and/or quantity of your samples DNA
Definitely, as you would save time and money if you check your DNA before shipping it to us.
We suggest that you follow the QC procedure we use (see above), testing for the quantity and quality of DNA as well as the lack of nucleases, on an agarose gel.
You may want to control further the suitability of the DNA for DArTseq, DArTseqLD and DArTcap by testing the digestibility of the DNA using a frequently cutting (e.g. 4bp recognition site) restriction enzyme, always running side by side cut and uncut DNA, in the same buffer.
You can find all relavent information for packaging orders on at http://www.diversityarrays.com/orderinstructions/. This includes how to package your DNA orders.
At DArT we try to expedite processing your orders as quickly and efficiently as possible, yet we still receive samples poorly packed or missing paperwork. Please contact us if you have any doubts or questions.
Markers | Back to top
DArT markers resulting from DArT sequencing platform (DArTseq, DArTseqLD, DArTseqMet, DArTcap, DArTag, DArTmp) are reported with marker sequence information. You can find a detailed description of marker types reported on our DArtSeq Data Types page.
As a legacy of the DArT microarray platform we maintain sequences of some microarray based DArT markers. For details, please visit our Sequences page.
Yes, we keep sequences of our initial DArT markers accessible via our website.
The largest volume of sequences were obtained for Barley, Oats, Sorghum, Sugarcane, Cucumber, Wheat, apple Rye and Eucalyptus. While we still have in our repository hundreds of thousands of original DArT clones we stopped sequencing them several years ago when we moved to services based on NGS platforms.
We produce mostly SNP markers using several different types of assays which cover a broad range of marker density and applications. Our DArTseq, DArTseqLD and DArTcap markers generate also “Silico DArT” markers which are complementary to SNPs generated on these platforms and increase significantly your ability to detect genetic signal in the sequence data. SNPs can be also typed on DArTmp and DArTag platforms.
Yes, our “targeted” assays like DArTmp and DArTag can adopt SNP assay from almost any current platform. Importantly, DArT will not deliver service for just one or a few markers as even our “low plex” platforms are designed to work effectively and offer significant cost savings compared to other platforms when the number of markers is at least above 30.
Ordering services | Back to top
There is no simple answer as DArT is a stickler for service quality and in some cases producing the best possible report for your samples takes a bit more than average time. However, our aim is to deliver a service within 7 weeks from the moment your DNA (or tissue) samples arrive and have met our quality requirements to proceed. In some cases that require faster processing (e.g. Genetic ID service and breeding applications), we can reduce the time required to under 3 weeks. Please alert us about your timelines so that we can incorporate it in our service execution planning.
Your samples need to be processed by the DArTseq production pipeline which consists of four main stages: Quality Control, Laboratory Assay, Sequencing, Marker Data Extraction and Report Generation.
This pipeline is in continuous operation as we process orders for clients in 60+ countries and hundreds of organisms. On arrival, after the initial QC step is passed, new orders are allocated a position in the processing schedule.
Our priority for every order is always Quality first, followed then by timeliness, therefore quality controls are implemented at every step of sample processing.
If DArT is performing DNA extraction for you, the time from sample arrival until report upload into the Online Ordering system can be slightly longer, depending on the organism involved, order volumes and again, the quality of the samples received.
Our preferred methods of payment are via:
- Direct fund transfer to our Australian accounts (The invoice number MUST be quoted in the reference or message section of the transfer form);
- Credit card – Visa, MasterCard, American Express, Diners, JCB (Note: A 3.5% surcharge applies); or
- Cheque (Made payable to Diversity Arrays Technology Pty Ltd).
Services are invoiced on your receipt of the data, however invoicing in advance and quotes are also available.
Please refer to the:
- “OUR REQUIREMENTS” and
- “SPECIAL CONDITIONS”
sections in the Sample Service Specification [PDF].
Practically all our services are delivered as a DNA to marker data (or tissue to marker data when ordering service with DNA extraction included). This means that users receive completely processed information, not just raw data.
In addition, one can order additional downstream analyses which add value to our services. Some relatively simple analytics can be provided free of charge (distance matrices, dendrograms etc) but we may have to charge you a fee for a more complex analysis. Please contact us if you want to extract more value from our service to you!