Genomics & Bioinformatics Core Facility

DNA Fragment Analysis Service

Order Submission Guidelines

Our DNA Fragment Analysis Service is a Ready-to-Run Service only for genotyping analysis using the Applied Biosystems 96-capillary 3730xl DNA Analyzer. The user completes the DNA Fragment Length reaction (i.e. microsatellite PCR) and submits the samples according to our Sample Preparation Guidelines. Please follow all instructions as detailed in the How to Order and Sample Preparation Guidelines to avoid sample-processing delays. Label on reaction plate and Order Form must be the same.

Drop-off your Order 

Open: 9:00AM to 4:30PM
DNA Fragment Length Analysis Freezer
Genomics Core Facility
Room 019 Galvin Life Science Center
Phone: (574) 631-1902

Failed Reaction(s) and Redo Policy

Contact us to address your questions/concerns, and we can discuss our failed reacion(s) and redo policy with you. We strive to provide high-quailty service; however, data quality is affected by a number of factors and variables. You can reach us by phone or email

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How to Order

Genomics Core Facility manages DNA Fragment Analysis Services using two interfaces: CORES System and Order Form

Order Form (Separate from Cores)

Order Form: DNA Fragment Analysis Service         Email to: by 12:00PM for 2- to 3-day business day service.

REMEMBER: Label on the "Plate" and "Order Form" must be the same.


  1. Go to CORE Login Page:
  2. Quick Links >  Select Order Entry
  3. Select > Genomics Core Facility - Pfrender, Michael
  4. Click on the FOP # to charge for the service.
  5. Fill out Order Entry by selecting Item Information Drop-down Menus:
    • Category > Capillary sequencing/analysis
    • Description> Ready-to-Run Sequencing/Fragment Analysis, reaction
    • Qty> Enter the number of reactions
  6. Click Add Item button to add items to the same order, and then repeat step 5.
  7. REQUIRED: Purchaser’s Information must be the same as Order Submission Form. Failure to complete the Purchaser’s Information will delay sample processing.
  8. Optional: Attachments can be added, but the Order Form must be emailed to
  9. Review your Order Entry. Be sure all information is accurate, and the Purchaser’s Information is correct.
  10. Click "Submit Order Request".

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Sample Preparation Guidelines

  1. Prepare your sample with compatible fluorescent dye label and DNA Size-Standard.
    1. For a list of compatible dyes and standards, see AB3730xl Compatible Fluorescent Dyes and Standards table.
    2. Depending on the dye and DNA Fragment Length combinations, several labeled products may be multiplexed (i.e. pooled) within a single reaction.
  2. For ready-to-run samples, submit your DNA Fragment Analysis samples in a labeled 3730xl-compatible 96-well plate suspended in the appropriate volume of AB Hi-Di Formamide. For a list of 3730xl-compatible 96-well plates, please see the ABI 3730XL Compatible 96-well Half-Skirted Plates table.
  3. Submit your samples and order form according to the How to Order and Sample Preparation Guidelines sections.


Distributor Catalog No. Description
Dot Scientific, Inc. 351-PCR PCR PLT 96W 0.2ML HS NAT PRINTED AXIS 10/PK
VWR 89126-694 96-Well PCR Plates, Neptune
Applied Biosystems 4316813 MicroAmp Fast Optical 96-Well Reaction Plate (0.1 mL)
ThermoFisher Scientific AB1400 Thermo Scientific 96-Well Semi-Skirted Plates, Flat Deck
ThermoFisher Scientific NC9009219 USA Scientific Inc  TEMPLATE III PCR


DNA Size-Standard (Color) AB Genescan Liz (Orange) AB Genescan Rox (Red)
Fluorescent Dye Label (Color)








NOTE: Sensitivity of the instrument for HEX Dye is poor, resulting in weaker peak signals than expected. Recommend loading more of your sample labeled with HEX for better results.

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For each sample well, one file is generated: *.fsa file. Files for all sample wells are copied to and accessible from the Genomic Data Folder for your laboratory.

Getting Your Results

To retrieve your results and data files, access the Genomic Data Folder for your laboratory. To access this folder, follow the instructions of how to map a network drive.

For Windows Operating Systems 7 or higher

  1. Begin from the Start Menu Button, and select File Explorer. A prompt window will open.
  2. From the top of the prompt window, click on the Tools Menu, and then select Map Network Drive. A prompt window will open.
  3. Within the Map Network Drive Window, select a Drive Letter from the field Drive List.
  4. In the field labeled Folder Box, type the path of the folder: \\\~genomics\Private\[your specific lab folder]
  5. User must enter the name of [your specific lab folder]. Typically, [your specific lab folder] is your PI’s name followed by “_Lab”.
    • Example: \\\~genomics\Private\Smith_Lab
  6. Click "OK".

For MAC Operating Systems OX10.5 and higher:

  1. Begin from the FINDER Window.
  2. From the top menu, click GO menu and then select CONNECT TO SERVER. A prompt window will open.
  3. In the field SERVER ADDRESS of the prompt window, type the path of the folder: smb://[your specific lab folder]
  4. User must enter the name of [your specific lab folder]. Typically, [your specific lab folder] is your PI’s name followed by “_Lab”.
    • Example: smb://
  5. Otherwise to obtain [your specific lab folder], contact us.
  6. Click "Connect".

To view your results, use one of the following available softwares:

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