DNA Extraction

Whole Blood and Buffy Coat

If possible, collect blood in EDTA tubes to reduce DNA degradation. However, other anticoagulants such ACD (citrate) and CPDA may also be used successfully. Heparin may be used but is not recommended.

The amount of DNA isolated from a blood sample is highly dependent on the number of white blood cells present in the sample and the blood storage conditions. On average, 350 ug of DNA is isolated from 10 ml of fresh blood sample. Samples frozen at -80°C typically exhibit a 15% decrease in DNA yield.

For short term storage, keep freshly drawn blood samples at 4°C for less than 5 days. For best results, the samples should be delivered to the core 1-4 days after collection. For long term storage, blood samples should be stored at -80°C soon after collection. The core facility does not recommend storing blood samples at -20°C for any length of time. Blood storage at this temperature for as little as 3 days results in decreased DNA yield. Storage at this temperature for 2-4 weeks results in half the yield as the same sample stored at -80°C.
 Buffy coat should also be stored frozen at -80°C prior to processing.

For more information on blood drawing, processing (including buffy coat preparation), and storage, please refer to the Guidelines of the National Heart, Lung and Blood Institute Working Group on Blood Drawing, Processing and Storage for Genetic Studies.

Buccal Swab

For best results, please select buccal swabs that have been reported to produce high-yield and high-quality DNA. Generic cotton or polyester swabs may result in low yields of DNA or DNA that contains inhibitors of downstream enzymatic reactions.

To collect enough cells for DNA extraction, vigorously rub the inside of each cheek or underneath the lower or upper lip for one minute. For most desirable results, deliver the swabs to the core for DNA extraction right after collection. If the swabs are to be stored more than one to two days prior to DNA extraction, they should be stablized. Our internal test shows DNA stabilization is crucial. In our hands, the Isohelix Dri-Capsules work well for the stabilization. 

Saliva

The source of DNA in saliva is buccal epithelial cells and white blood cells. To extract DNA from saliva samples, they should be collected with the Oragene Discover collection kit from DNA Genotek (OGR-500). For best results, the collected saliva should be delivered to the core within five days of collection. Saliva samples collected with the Oragene kit can also be stored at room temperature or frozen at -20°C or -80°C (but not at 4°C).

DNA extraction orders are submitted through the NUcore ordering system. Follow the directions below to submit an order through NUcore:

1. Go to https://nucore.northwestern.edu/facilities
2. Click on “Login” at the top right-hand side of the page
3. Enter your NetID and password
4. Click on “NUSeq”
5. Click on the link for the service you want (Example: DNA Extraction 1-5 ml)
6. Click “Add to Cart”
7. Select the payment source (chartstring number) and click “Continue”
8. Enter the quantity and click “Update”
9. Fill out and upload the completed order form
10. If your order is complete, click on “Purchase”, otherwise click on the “Home” tab on the top left-hand side of the page and repeat Steps 4 through 10

The Autopure LS System processes eight or 16 samples at a time. We suggest to submit sample numbers in multiples of eight. Since eight samples' worth of reagents is still consumed when there are less than eight samples, we charge for eight samples under such circumstances.

Please submit samples in secure tubes with clear labels or barcodes and specify volume of each sample (1-5ml or 5-10ml). These label should be able to withstand -80C temperatures. We do not recommend storing blood tubes in styrofoam before freezing at -80C; The bottoms of tubes can crack.

Freeze samples prior to packing, and ship with sufficient dry ice to ensure they remain frozen. This is to avoid the possibility of cross-contamination or degradation. We cannot accept samples for any study that have thawed or were not shipped frozen.

We recommend that you completely fill the shipping container with dry ice to minimize air space. We also recommend that you pack samples in cardboard freezer boxes placed in large plastic bags to protect samples from dry ice, and use dry ice pellets rather than blocks to avoid damage during shipment.

Include a packing list containing sample IDs, sample type, cell count (if applicable) and box number and position. Please forward an electronic version of this packing list as well so we can have a copy for our records. If necessary, also include any special instructions for the handling of your samples.

There are several ways you may send your samples to the core:

If you are from Northwestern and are on the Chicago campus:

Bring your samples directly to the facility's lab location. Fresh samples brought directly to the Core should be stored in the DNA Extraction room refrigerator. Please drop off samples directly to a technician at the Core if they need to be stored at -80°C.

If you are from Northwestern and are on the Evanston campus:

Drop your samples off at one of the two courier locations in the Hogan Building, 2205 Tech Drive: Hogan 2-100, BMBCB administrative office, or Hogan 4-150.The couriers pick up the samples every morning and we receive them in the afternoon.

If you are not on the Northwestern campus:

Please send your samples through an independent carrier such as FedEx or UPS to the address listed under contact us. Prior to shipping, please contact a technician to schedule delivery. At the time of shipping, please send an email notification with your express mail tracking number. This will allow us to watch for your shipment. We prefer that samples are sent overnight on Monday or Tuesday so that we can guarantee someone is here to accept them. We will notify you when your shipment is received.

Turnaround time varies with the size of your project. Please contact us for more information.

The core will deliver aliquots of your samples after extraction in 1.5ml RNAse-free microcentrifuge tubes labeled with the PI name, extraction date, and sample ID unless requested otherwise. If you require different tubes, please provide these and the necessary labels.

The NUSeq Core retains submitted samples for two weeks following the completion of a project. If you would like the remainder of any sample to be returned at the completion of the project, please notify the core technicians when you submit your samples and they will be marked for return. Please collect the samples from the cre within two weeks of receiving your results. After that time, the samples will be disposed of. The core will not send reminders prior to disposing of the samples.