Instructions for online sequencing submissions

PLEASE NOTE: Due to recent events and the continuing concerns posed by potential bioterrorism agents, we have modified our online submission form to require that you provide us with information on the original biological source of any DNA that you will be asking us to obtain sequence from. "Original biological source" refers to the organism from which the DNA was first found in nature (human, HIV, Staphylococcus aureus, etc.). If you simply put a nonspecific term such as "E. coli clone" or something similar, this will not be sufficient. Further, we will not be able to accept DNA sequencing orders for select agents, until our legal responsibilities are clarified. Our current understanding is that, in order to receive select agent DNAs from you for sequencing, we would need to have a select agent permit, which we do not possess. We realize that adding yet another field to fill out on these forms can be tiresome, but this information is necessary to protect our staff against potential legal difficulties. Thank you very much for your understanding.

            - David W. Dyer, Ph.D.

 

 THE FOLLOWING REQUIREMENTS MUST BE MET BEFORE YOUR SAMPLES CAN BE SUBMITTED

Preparation of samples

1. All samples must be submitted in 96-well format (V-bottom plates or non-skirted PCR plate).
   
   
2. If you are submitting <96 samples, then load the plate in column format (i.e. A1-H1, A2-H2 etc.) Partial plates can be reused for submission, in which case you can use the first available column (i.e. starting with A4-H4 etc.) Just be sure that if you start with A4 on your plate you also begin with A4 on the submission form.
   
   
3. Each well should contain DNA and primer for only one reaction. Total volume in each well should be 4µl as described below.
   
   DNA template should come to a final volume of 3µl* (see concentrations below)
   
   Primer = 1µl (3.2 pmol/µl stock)
   
   *Plasmid DNA total concentration should be 500-600ng per reaction for templates the size of pUC (~2.9kb). Larger templates (>15kb) may require a higher concentration.
   
   *PCR products (use 10ng/100bp of product)
   
   
4. If you are using universal primers (see list below), then the directions above still apply. The facility can provide universal primers in 100µl aliquots (3.2 pmol/µl), currently free of charge.
   
   

   M13F	5'-TGT AAA ACG ACG GCC AGT-3'
   M13R	5'-CAG GAA ACA GCT ATG AC-3'
   T7	5'-TAA TAC GAC TCA CTA TAG GG-3'
   T7 Term	5'-GCT AGT TAT TGG TCA GCG G-3'
   T3	5'-ATT AAC CCT CAC TAA AG-3'
   SP6	5'-GAT TTA GGT GAC ACT ATA G-3'
   SK	5'-CGC TCT AGA ACT AGT GGA TC-3'
   KS	5'-TCG AGG TCG ACG GTA TC-3'
   PGEX3'	5'-CCG GGA TGT GTC AGA GG-3'
   PGEX5'	5'-GGG CTG GCA AGC CAC GTT TGG TG-3'

   
   
5. An SUR# (OUHSC) or PO# (off-campus) must be given at the time of submission.
   
   For samples that need to be shipped, please dry down your template and primer mix in a PCR plate before sending to reduce the chances of sample loss during shipping.
   
   Shipping Address:
   
   The Laboratory for Genomics and Bioinformatics OUHSC
   Attn: Nicole Benton
   975 NE 10th Street, BRC1106
   Oklahoma City, OK 73104
   


6. An on-line submission form must be filled out completely.

If the above 6 requirements are not met, your samples will not be sequenced

 

 TO KNOW

1. Turnaround time for customer sequencing is dependent on the number of samples we receive each day. Customers can expect their data within a maximum of 48 hours from the end of the day that the samples are received (not including weekends, or holidays). For example, samples that are received on Monday by 4pm will be ready for download no later than 5pm on Wednesday. Larger orders of multiple plates may take longer than 48 hours to complete, but data will be made available for download as each individual plate is processed.
   
   
2. Finished data can be accessed on the facility's website.
   
   
3. Samples are named automatically according to the well position in which it was submitted. (Example: the sample in well A1 will be named "a01")
   
   If you submit plates containing gaps between samples within a column you will be charged the regular sequencing rate for these gaps.
   
   
4. Finished sequences will be named as follows:
   
   date of run+run#_well#_sample#_capillary#.file type
   example: 2002062101_A01_a01_001.ab1
   - - [note: the date is set up as (YYYY/MM/DD)]
   - - [note: the well# has capital letters while sample# has lower case letters]
   
   Be sure to pay attention to the sample# since that number will correspond to the well position in which you submitted your sample. The well# on the finished sequence name will not always be the same as the sample#.
   
   
5. For a plate of reactions, we typically see an efficiency of 80% or better. This efficiency will vary, however, with different templates. Efficiency is expected to drop with more difficult templates, such as : AT or GC rich templates.
   
   
6. Once the samples have been sequenced, leftover templates and primers should be picked up within 2 weeks.
   
   
7. If you would like to pick up partial plates for re-use, please indicate in the special instructions of your order that you would like your plate saved for pickup. Remember that when plates are submitted with only certain parts of the plate covered, water may collect in uncovered wells during freezer storage. Reuse those plates at your own risk. We ask that people only take back plates that were submitted by them. We cannot be held responsible for lost or stolen plates. If you have any questions, please feel free to contact Nicole Benton.

 

 SUBMISSION FORMS

             online submission form   (for single plate submissions)

             high-throughput submission form   (for multiple-plate submissions)