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).
- 15 μl of required concentration (see below) for first sample/primer combination. For each subsequent primer with the same sample add 5 μl of sample. Example: 1 sample run with 2 primers would require at least 20 μl total sample volume at the indicated concentration.
- 1.5ml tube: Clearly labeled with Sharpie type pen, alphanumeric designation 3 letter initials and a unique number identifier (maximum 6 total digits for sample name). Do NOT use lab tape, write directly on tube. Example: TLM223, Tube and order form sample names MUST MATCH.
- 96 or 384 well plate: Large lots of samples can be submitted in 96 or 384 well plates. Plate map spreadsheets must accompany any plated samples. We recommend sealing 96-well plates with strip caps for shipping. Spin down and freeze, ship overnight on ice.
Large projects (>96 samples) please notify facility 2-3 weeks in advance.
Double-stranded DNA 100 ng/ul
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'
Repeated Submissions: To reduce waste we recommend sending aliquots (>200 μl) of primer, we will store and track individual lab primer stocks.
- The Genomics Core Lab will keep samples stored at -20 °C for 2-4 weeks.
- 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)