Fragment Analysis Services

gel imageThe DNA Core, using the ABI 3730xl DNA Analyzer, has the capability to rapidly size DNA fragments, such as, microsatellites (random 2-6 base pair repeats) and AFLPs (amplified fragment length polymorphisms). The ABI 3730xl DNA Analyzer allows for the use of a fluorescence-based detection system that automates the process of sizing DNA fragments. Fluorescent dyes are incorporated into the DNA fragment using fluorescence-labeled primers. An internal lane standard that ranges from 20-600 bases (Genescan 600 LIZ) is added to each sample for precise sizing of each fragment adjusting for lane to lane variation. A distinct advantage to the fluorescence-based system is the availability of four dyes allowing the multiplexing of multiple samples in a single lane. Eight samples can reliably be multiplexed in each lane of a 96-lane gel allowing hundreds of loci to be analyzed in a single day.

......Per Injection Cost......
Single Tube Submission $1.35/lane
96-well Plate $100.80 ($1.05/lane) *charged as whole plate

Submission Guidelines for Single Samples
  • Submit 3.0 ul of amplified PCR product in a 500 ul tube. Lane standard will be added to each well by core staff. Generally, the data will be ready the same day the samples were processed.

  • Note: If samples are being submitted in a 96 well format, please contact the DNA Core staff before submitting the samples so you can receive the correct 96 well plate required for our robotics. Sample volume of amplified PCR product in each well should be 2 ul.

Steps for Submitting Samples
  1. Fragment analysis orders are placed on-line using the DNA Core's dnaLIMS system.

  2. When properly submitted each order receives an order number and each sample recieves a requisition number. Label tubes with the last three digits of the requisition number on the top of the tube.

  3. For example: Order #15759 has two sample; Requisition #289573 and Requisition #289574. Each tube is labeled with the last three digits of the requisition #.

    Requisition #289573

    Requisition #289574

  4. Place samples in a plastic bag with the principle investigator's name written on the outside of the bag and order number. (Plastic bags are available at the DNA Core drop-off location (room 215, Life Science Center).

  5. Place samples in refrigerator at DNA Core drop-off location (in hallway across from room 211, Life Science Center).

Primer Selection Guidelines
  • Primers should be chosen that are 15-30 nucleotides with similar melting temperatures. A GC content of 40-60% is recommended due to an increased melting temperature and annealing specificity. Also, primers should be checked for dimers and hairpin structures. Secondary structure check and Tm calculation can be performed using Oligo Analyzer 3.0 on the Integrated DNA Technologies web site.

  • Important Note: The DNA Core recommends using 5'-end labeling of fragments. The core utilizes the standard dye set DS-33 from Applied Biosystems. The lane standard used with this dye set is labeled with LIZ(orange). Primers are to be labeled with 6-FAM(blue), VIC(green), NED(yellow) or PET(red).