Genomics & Bioinformatics Core Facility

DNA Sanger Sequencing Ready to Run

Our Ready-to-Run Service option includes samples ready to sequence on the Applied Biosystems 96-capillary 3730xl DNA Analyzer. The user completes the DNA Sanger reaction preparation and submits the samples according to our Sample Preparation Guidelines. Please note sample plates are discarded after data is delivered.

Looking for resources to help you troubleshoot your DNA sequencing reactions? Please see our Troubleshooting Resources page. 


Submitting Your Order

Genomics Core Facility manages all DNA Sanger Sequencing Service using two interfaces: CORES Ordering System and Sample Information Form.
For 2- to 3-day business day service, enter your order into the CORES Ordering System and send your Ready-to-Run Sample Information Form to genomics@nd.edu by 12:00PM, and samples must be delivered to our faclity by 2:00PM. 

CORES Order Entry

NEED TO SETUP A NEW RESOURCE USER IN CORES: Resource guides are available from the Facilities and Resouces page of Notre Dame Research.

  1. Login to CORES.
  2. From the Order Entry Panel, enter into the field your Last Name or FOP. Click Search button.
  3. Select the appropriate CORE Facility: Genomics Core Facility - Pfrender, Michael
  4. Select the appropriate FOP from the list.
  5. Complete the Order Entry –Item Information:
    1. Select the Category from the drop-down menu
    2. Select the Description from the drop-down menu
    3. Enter the quantity.
  6. Click Add Item button to entry additional items to the same order, and then repeat step 5.
  7. REQUIRED: Purchaser’s Information must be populated with your Last Name, First Name, email address, and phone number.
    1. Choose your own name from the Purchaser's drop down menu. If your name is not populated in the drop down, replace the default Last Name and First Name fields with your information. When the order is submitted, data will be delivered to the Purchaser Listed. Failure to complete the Purchaser’s Information will delay sample processing.
  8. Review your Order Entry. Be sure all information is accurate and the Purchaser’s Information correct.
  9. Click Submit Order Request.

Ready-to-Run Sample Information Form

  1. Download Ready-to-Run Sample Information Form for DNA Sanger Sequencing.
  2. Send your completed form to genomics@nd.edu by 12:00PM for 2- to 3-day business day service.

Sample Delivery

To avoid sample-processing delays, ensure your tubes/plates are clearly labeled with your initials, date, and sample number. Deliver your samples to our Genomics Core Facility by placing them in our designated DNA Sanger Sequencing freezer. Please note sample tubes/plates and primer tubes are discarded after data is delivered.

Deliver your samples by no later than 2:00PM (EST-D) to our facility:

Genomics Core Facility
Galvin Life Science Center Room 019
Phone: (574) 631-1902

 

Sample Preparation Guidelines

  1. For ready-to-run samples, submit your DNA Sanger Sequencing products 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 AB3730xl Compatible Plates section.
  2. Submit your samples and order form according to the Order Submission Guidelines and Sample Submission Guidelines.

AB3730 Compatible 96-well Half-Skirted Plates

Distributor

Dist. Catalog

Description

Dot Scientific, Inc.
351-PCR
PCR PLT 96W 0.2ML HS NAT PRINTED AXIS 10/PK
ThermoFisher Scientific
AB1400
Thermo Scientific 96-Well Semi-Skirted Plates, Flat Deck

Results

For each DNA samples, two files are generated: *.abi file and *.seq file. Both files will be copied to and accessible from the Genomic Data Folder for your laboratory.

Failed Reaction(s) Policy

We agree to re-run failed reactions using the same template and primers, upon your request. If the reaction fails again, you will be charged for both the initial reaction and the second requested reactions. Otherwise, you will be charged only for the successful reaction.

Getting Your Results

To retrieve your results and data files, access the Genomic Data Folder for your laboratory. To access this folder, follow the instruction 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:
    1. \\fs.nd.edu\~genomics\Private\[your specific lab folder]
    2. User must enter the name of [your specific lab folder]. Typically, [your specific lab folder] is your PI’s name followed by “_Lab”.
    3. Example: \\fs.nd.edu\~genomics\Private\Smith_Lab
    4. Otherwise to obtain [your specific lab folder], contact us.
    5. Required: Select Connect Using a Different User Name. In the field User Name, enter ADND\[your ND net ID] and enter your ND Password.
  5. Click OK and then Finish.
  6. The mapped folder will appear in the File Explorer window.

For MAC Operating Systems OX10.5 and higher:

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

Viewing Your Results

Sanger Sequencing Software

Applied Biosystems Sequence Scanner Software v2.0 (Download)
Operating System: Windows 7
Description: View, edit, print and export data generated using AB37030XL and other Applied Biosystesms Genetic Analyzer instruments. 

QIAGEN CLC Sequence Viewer (Download)
Operating System: Windows Vista, Windows 7, Windows 8, Windows 10, Windows Server 2008, or Windows Server 2012; Mac OS X 10.7 or later
Description: View, edit, and manipulate data generated using AB37030XL and other Applied Biosystems Genetic Analyzer instruments. For a complete list of features, click here

Sequencer 5.1 (Download)
(Notre Dame Faculty / Staff / Students only)
Operating System: Windows; Mac OS X
Description: View, edit, print and export data generated using AB37030XL and other Applied Biosystesms Genetic Analyzer instruments.
Required Utility Software:  To run Sequencher, KeyAccess client must be installed. Downolad here.
Remote Access Uility Software: To remotely access Sequencher, Cisco Clean Access VPN connection is required when off-campus. Download here.
 

Fragment Analysis Software

Applied Biosystems Peak Scanner Software v2.0 (Download)
Operating System: Windows 7
Description: DNA sizing software to perform fragment analysis, separate a mixture of DNA fragments by size and provide a profile of the seperation. View, edit, print and export data generated using AB37030XL and other Applied Biosystesms Genetic Analyzer instruments. 

Applied Biosystems Sizging Analysis Module, Peak Scanner Software (Go to Cloud)
Operating System: Free access on Thermo Fisher Cloud
Description: DNA sizing software to perform fragment analysis, separate a mixture of DNA fragments by size and provide a profile of the seperation. View, edit, print and export data generated using AB37030XL and other Applied Biosystesms Genetic Analyzer instruments. 

Resources

Ready-to-Run Sample Information Form