Denghui David Xing, Ph.D.
Genomics Laboratory Manager
ISB 321(office) & 007 (Lab)
We run positive controls with every sequencing and fragment run. We will rerun any failed sequences deemed necessary by the investigator. If the sample gives the same results from an identical rerun, the account will be charged for both runs. If the sample gives good sequence from an identical rerun, there will be only one charge to the account. Please call if you have any questions.
(terms and conditions link)
Mailed sample submission: Make sure to note in your sample request form when samples will be shipped.
ABI 3130 Genetic Analyzer
Template should be submitted with all samples normalized to required concentrations (see chart below).
- For orders with <48 samples, please use 8-strip PCR tubes to streamline preparation and processing. Label your tubes on the side with your initials and sample number. For orders with ≥48 samples, please using a 96-well PCR plate and arranging the samples vertically (A1 to H1).
- Dilute your sequencing primer to 5 µM (5 pmol/µl) using water. If you want to use a UMGC Universal Primer, we will add it for you at no charge.
- For the amount of template needed in each of our DNA Sequencing Services, please refer to the tables below. Prepare template in 10 µl for each sequencing reaction. Please make dilutions in water or Tris-HCl (pH 8.0). (Note: For best results, do not use Tris-EDTA (TE) because EDTA will inhibit the sequencing reaction).
- Pre-mixed your sample and primer. In the same tube, mix template (10 µl) and your primer (5 µl) according to the table below. To use a UMGC Universal Primer, simply submit template at the requested concentration in 10 µl.
Large projects (>96 samples) please notify facility 2-3 weeks in advance.
M13R(-48) 5' AGC GGA TAA CAA TTT CAC ACA GGA 3'
T7 promoter 5' TAA TAC GAC TCA CTA TAG GG 3'
SP6 5' ATT TAG GTG ACA CTA TAG 3'
T3 5' ATT AAC CCT CAC TAA AGG GA 3'
- The Genomics Core Lab will keep samples stored at -20 °C for 1 week.
- Reruns must requested ASAP after initial run (email: firstname.lastname@example.org with requests to re-run)
Fragment Analysis (3130 Genetic Analyzer)
We run fragment analysis on batches of 16, or multiples thereof. Submissions with less than 16 samples will be charged 16 lanes.
Submitting your samples:
You can select from three different size standards at this time, depending on the markers you have chosen for your labeled primers.
- GS600LIZ – can use markers labeled with 6-FAM (blue), VIC (green), NED (yellow), PET (red).
- GS500ROX –can use markers labeled with 6-FAM (blue), HEX (green), NED (yellow).
- MM1000ROX—can use markers labeled with 6-FAM (blue), HEX (green), NED (yellow).
The Genomics Core will supply plates unless the user wishes to purchase the specialized plates from a vendor. Please contact the core to make sure plates are compatible prior to purchase.
Sanger Sequencing and Fragment Analysis Data Retrieval
If you are a new client you will need to request a username and password for access.
To access your results you will need to download a dedicated secure ftp application. You cannot enter the sftp host address into your web browser address line, as this is not a web recognized URL.
There are several freeware applications available. One we are familiar with is FileZilla. (***NOTE*** This is an external link)
Once you have the Filezilla software open, enter in the Host: sftp://murdocklab.dbs.umt.edu, the user and password below to enter the secure ftp site. You should be able to find your results folders in the lower window on the right side ("remote site") of your Filezilla window. Then click on your file and drag it to your computer files which are displayed in the left hand window of Filezilla as “local site". Let me know if you have any problems or questions.
Please let me know if you have issues connecting.
Sequencing Data Analysis:
There are numerous freeware sequence viewing software available that may support your needs. Be aware, we do not support these programs. They are some of that have come to our attention via UMGC users.
ABI Sequence Scanner (pc)
CodonCode aligner (Mac)
4 peaks (Mac)