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DNA Fragment Analysis: Sample Submission


Sample Preparation:

  • Please provide a total of 10 ul for each DNA fragment sample.

  • Fragments should be labeled with NED, 6-FAM, PET, or VIC. Our instruments are calibrated for use with Dye Set DS-33 (filter set G5) and will not optimally support other dyes. The LIZ channel is reserved for our size standard.

  • In most cases, purification of the sample is not required. However, if residual contaminants or artifacts should interfere with accurate size assignments, purification of the PCR reaction should be considered by the researcher.

  • Please prepare samples in 1.5 ml tubes or in a 96-well plate according to our specifications (see below).
    Please note: We have discounted pricing available for full plate (bulk) orders.

Tube Orders:

  • If you are submitting your samples in tube format, please use standard 1.5 ml flip-cap Eppendorf-type tubes.
    Please note: Our operational setup does not accept 0.2 ml tubes, 0.5 ml tubes, strip-tubes, and screw-cap tubes.

  • Please label the top of the lid of each tube - as clearly as possible - with a maximum of 5 alpha-numeric characters (for example: 5B001). We strongly recommend hand-writing each label using a permanent marker. Self-adherent stickers might fall off during shipment, thereby making sample identification impossible.

  • Tubes (to be submitted in a sample box or sample rack) must be sealed properly and wrapped in foil. We also recommend wrapping each individual tube with Parafilm to prevent samples from drying.

  • Place your Fragment Analysis Order online and include a printed copy of the barcoded order form with your sample submission.

    Tubes should be submitted in order as listed on the submission form (not randomly placed, and not loose/unracked).
    If you are using one of our remote drop-off locations, please rack your tubes in one of the provided sample boxes and attach order form with a rubber band. If for some reason no boxes should be available, please tape tubes to the order form (or a separately attached sheet) in the same order as listed on your order form. You may also use any other type of rack/box designed to hold 1.5 ml tubes.

Plate Orders:

  • If you are submitting your samples in plate format, please use only V-bottom PCR plates.

  • We recommend the use of semi-skirted (or skirted) plates to prevent the PCR plate from bending during transit, which could result in loosening of the seal and subsequent sample loss and cross-contamination.

  • Please arrange your samples horizontally (in rows) in the PCR plate. Proceed from well A1 to A12, from B1 to B12, from C1 to C12, etc.

  • Please do not leave any empty wells between samples, and please do not leave any empty spaces between samples on the order form.

  • The order form must match the order and position of samples in the PCR plate.

  • Please label the plate as clearly as possible - with a maximum of 5 alpha-numeric characters (for example: 5B001).

  • Tightly seal your plate(s) with an adhesive sheet/foil to prevent samples from drying and/or cross-contamination.

  • Place your Fragment Analysis Order online and include a printed copy of the barcoded order form with your sample submission.

Sample Concentration:

The detection capability of the ABI 3730XL is highly sensitive, and an excessive DNA fragment concentration of a sample can interfere with data collection and subsequent analysis. Determining the optimal sample concentration for ensuring high-quality results is the responsibility of the investigator submitting samples to our core facility.

For any new Microsatellite/MLPA assay, we highly recommend submitting a dilution series first:

  • 2 samples at full-strength (original PCR reaction)
  • 2 samples with 1:10 dilution of original PCR
  • 2 samples with 1:50 dilution of original PCR
  • 2 samples with 1:100 dilution of original PCR


We accept the submission of multiplexed samples (i.e. samples containing fragments labeled with different dyes) for our ready-to-run DNA Fragment Analysis service. However, we are not offering on-site data interpretation in this case.
Please note: When submitting multiplexed samples to our facility, you MUST select “N/A” from the pull-down menu in the “Dye” column to avoid being automatically charged the additional analysis fee.

Sample Shipment:

Please submit your sample(s), including a hard copy of the completed order form, by using one of our remote dropboxes (please see here) or by delivering it personally to our core facility.

If remote or direct sample drop-off should not be an option for you, please ship your samples, including a hard copy of the completed order form, via a courier delivery service of your choice (for example, overnight shipment via FEDEX, UPS, etc.) to our core facility. Samples can be shipped at ambient temperature.

Shipping Tubes:

Unfortunately, we often receive sample tubes that were damaged during shipment (cracked or shattered tube, sample loss due to leakage or evaporation). Therefore, we strongly recommend sealing the sample tube with Parafilm and further protecting it with bubble wrap or several layers of Kimwipe tissue. Another option is to place the sample tube into a secondary container such as a Falcon tube or small cardboard or plastic box.

Shipping 96-well Plates:

Samples should be arrayed in a 96-well (semi-skirted or skirted) plate. To prevent sample loss and/or cross contamination, we recommend tightly sealing all wells of the plate with Microtube Caps. PCR Tube Strip Flat Caps (Eppendorf cat# 0030124847 or VWR cat# 75874-710) work well for most plates. Our everyday experience tells us that plate foils/plastic seals can partially lift off or even entirely detach during transit dependent on the shipping conditions (heat, air pressure, humidity, etc.). Please place your plate in a corrugated box for maximum protection.

Shipping Address:

MGH CCIB DNA Core Facility
38 Sidney Street, Suite 100
Cambridge, MA 02139

IMPORTANT: Please note that we are not receiving samples on Saturdays and Sundays or on official holidays.