Fragment analysis

Microsatellites, SSRs, and other fluorescently-labeled PCR products can be sized on our ABI 3730xl DNA Analyzers. Up to four fluorescent dyes, in addition to the size standard, can be detected. Currently, we run the Applied Biosystems G5 dye set (6-FAM, VIC, NED, PET, and LIZ). For this service, you must supply your sample plates with the fluorescent size standard already added and we accept samples only in 96- or 384-well plates that can be directly loaded onto the DNA Analyzers.

The correct semi-skirted 96-well PCR plates can be purchased from either Fisher Scientific (catalog number 14230244) or USA Scientific (catalog number 1402-9200 or 1402-9300). Other plates that are compatible with the ABI 3730 instruments are acceptable. If you have a plate that you think is compatible, please email us a picture and we will let you know if they will work. For samples submitted in an incorrect plate, there will be a fee charged for transferring your samples to the correct plate. Also, submitting samples in the wrong plates will delay the processing or your samples.

Link to Genomics Price List

Fragment Analysis and RTL Submission Guidelines: FA/RTL guidelines

Typical mixtures for Fragment Analysis (in each well of the plate):

1 ul PCR product (this is typical, but you may have to optimize for your reaction products)
0.2 ul LIZ 500 size standard (this is the expected size standard....others may be used, but the lab will have to be notified if another is used)
Bring volume up to 10-20 ul with HiDi formamide (available from ABI/LifeTech)

All wells in the plate must contain liquid. Wells with no samples should contain 10-20ul ddH2O or formamide. Also, the plates should be sealed well to prevent evaporation.

More information on submitting Fragment Analysis orders can be found at this link: Fragment Analysis Ordering

There are several software packages available for fragment analysis. These include PeakScanner from ABI, and GeneMarker from SoftGenetics. Please contact the Genomics lab for information on access to, and using, these different software packages.

 

Link to Genomics Price List