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Fragment Analysis

Fragment Analysis Submission Policies

Our DNA Analyzer uses fluorescence based detection to determine the size of DNA fragments. We will add the size standard and perform the electrophoresis on the samples.

- All samples must be submitted in 96-well plates.

  • ABI MicroAmp Optical Plates, part #N801-0560.
  • USA Scientific TempPlate #1402-9596
  • Eppendorf Twin Tec PCR Plate #951020303
  • Thomas Scientific Non-Skirted PCR Plates #1148A37

**Fast plates will not work with our instrumentation and will require samples transfer to a compatible plate.

ABI #4346907 and VWR 82006-664 are two examples of incompatible plates.

If you have questions about plates other than those listed above, please contact and we can determine compatibility.**

- Plates must be sealed properly and wrapped in foil.

- After the order is placed online, please email us the sample sheet. If a sample sheet is not supplied, your sample files will be named Plate Name-Well number.

- Please click on link for the appropriate dye set.

- We currently accept samples labeled with the following dye sets:

  1. DS-30: 6-FAM, HEX, NED and ROX, where ROX is the size standard. [Template]
  2. DS-33: 6-FAM, VIC, NED, PET and LIZ, where LIZ is the size standard. [Template]
  3. DS-02: dR110, dR6G, dTAMRA, dROX and LIZ, where LIZ is the size standard. [Template]

Fragment Analysis Submission Protocol

(1) Before pooling multiplex PCR products:

  • We recommend running a mini-gel to verify that your PCR product works.
  • Determine optimal PCR concentration by serial dilution.
  • Example of possible Microsatellite optimized concentration: pre-PCR = 50ng/µl, post amplification 25ng/µl
  • To avoid Plus A problem order primer with tails. See User Bulletin: Plus A Artifacts for more information.

(2) Submission:

  • Internals: 1-2 µl of each fluorescently labeled PCR product brought to a final volume of 10µl with water or HiDi Formamide.
  • Externals: 1-2µl of each fluorescently labeled PCR product brought to a final volume of 10µl with water.

Fragment Analysis Applications

  1. Microsatellite Analysis Fact Sheet: 106MI61
  2. BAC Fingerprinting on 3730/3730xl
  3. Screen for loss of heterozygosity

Standard Turn Around Time

Standard turnaround time is 1 business day. Results for Yale researchers can be viewed using GeneMarker or GeneMapper software through a remote desktop connection. Please email us at for login instructions.