The Applied Genomic Technologies Core

Fragment Analysis

The AGTC performs and optimizes PCR for agarose gel-based genotyping and fluorescent fragment analysis including Amplified Fragment Length Polymorphisms (AFLPs).

DNA Analyzers

• Applied Biosystems 3730 DNA Analyzer (96 capillary instrument)
• Applied Biosystems 3100 DNA Analyzer (16 capillary instrument)

Supported Dye sets

• (G5): 6-FAM, VIC, NED, PET, LIZ
• (DS-30): HEX, NED, 6-FAM, ROX
• (DS-31): VIC, NED, 6-FAM, ROX

Thermocyclers

• 6 MJ Dyad dual block
• 4 Techne Genius

Automated Workstations

• Perkin Elmer Multiprobe II Automated Workstation
• Perkin Elmer Janus
• Perkin Elmer Evolution EP3

Throughput

• 1440 samples in a 24hr period

Analysis Software

• Genotyper (ABI)
• Genemapper (ABI)
• Genemarker (Soft Genetics)

Guidelines

Please contact a member of the AGTC staff before you submit a request for service that has never been performed within the Core.

Complete the Sample ID Sheet and Service Request form whenever you submit samples to the AGTC.  Please consult with the AGTC Genotyping staff to determine the best approach for this service submission. 

Sample Submission

Samples may be submitted using one of the two options below.  When possible, use the same buffer for re-suspension/dilution.  An additional charge will be applied if it is necessary to transfer samples to appropriate lab ware. 

1. 96-well format: fill columns before rows and assign unique sample names and plate IDs

• Plate = AB-Gene 96-well plate cat # AB-1100.
• Caps = AB-Gene 8-strip cat # AB- 0602 or 12-strip cat # AB- 0853.
• Sample = Concentration and amount of DNA is assay specific, please consult AGTC Genotyping staff
• Buffer = T.E. (10mM Tris HCl, 0.1mM EDTA, pH 8.0) or dH2O.
  

2. 1.5ml Tubes

• Tubes = 1.5ml clear Axygen cat # MTC-150-C.
• Sample = Concentration and amount of DNA is assay specific-consult AGTC Genotyping staff
• Buffer = T.E. (10mM Tris HCl, 0.1mM EDTA, pH 8.0) or dH2O.

Reagent Submission

• Primers may be submitted to the AGTC directly or after receipt from the manufacturer. 
• Follow all handling instructions associated with the reagents. 
• If submitting primers that have already been re-suspended and/or used please indicate the concentration, buffer used to dilute or re-suspend, and the storage conditions (if different from the manufacturers recommendations).

Control Submission

The Core strongly advises the submission of controls for all possible genotypes.  The samples that are submitted by the investigator as controls are used when testing the quality of the assay and without proper controls, it is impossible for the Core to properly determine the assay’s true quality.