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UC Berkeley DNA Sequencing Facility FAQ
303 Barker Hall #3202
Berkeley, California 94720-3202
dnaseq@berkeley.edu
(510)642-6383

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I don't know anything about chartstrings or fund numbers.
Call your accounting department. If that is not possible or convenient, call us 510.642.9601. We don't want the accounting details to get in the way. We will run your samples today and help you get the accounting straightened out later.
 
What size tube should I put my mix of template and primer in?
1.5mL tubes are the easiest for us to handle. Try to avoid .2 mL tubes, for they are the most difficult to handle
 
How do I view my chromatogram files?
NOTE: ALL of your files should open, and there should be NO odd characters or symbols in the .seq text files. If either of these things happen, you probably need us to send your files in a different format (BinHex instead of MIME). This problem occurs most often with people using MACs that get there e-mail through CalMail. If this sounds like you, contact us. Files can get mixed up if your computer cannot read MIME format through CalMail.

There is free software available on the internet that will allow you to view your results.

PC users can go to these websites:
Sequence Scanner from Applied Biosystems: https://products.appliedbiosystems.com Sequence Scanner works on XP and Windows 2000.

or
Finch TV: http://www.geospiza.com/finchtv/ FinchTV works on OS X and Windows.

or
Chromas http://www.technelysium.com.au/chromas14x.html

MAC users can go to these websites:
4Peaks: http://www.mekentosj.com/4peaks/ 4Peaks works on OS X.

or
Finch TV: http://www.geospiza.com/finchtv/ FinchTV works on OS X and Windows.

or
Edit View works on OS 9.

MAC users may also need to use conversion software (before opening files with Edit View) available for free by clicking on this web link. Instructions for how to use the conversion software can be downloaded from the same web link as the software.
If that web link does not work follow these directions:
Go to www.appliedbiosystems.com.
Click on "Services & Support".
Click on "Software Dowloads".
Under "Select Product Software", use the drop down menu to choose "ABI PRISM 3100 Genetic Analyzer"
Under "Select Software Type", use the drop down menu to choose "Conversion Utility"
Download "3100 Conversion Utility".
And "3100 Conversion Program Notes"

Let us know right away if you have any trouble viewing your files.
 
When will I receive my results?
We will notify you via email. Samples turned in before 11:10am at 237 Stanley and 11:30 at 317 Barker or 136 LSA will be ready by the afternoon the next business day.
 
What are your suggested DNA concentrations?
The suggested DNA concentrations are:
(A) 0.25 microgram DNA / 5kb SS plasmid + 2 pmol primer in 13 microliter, 1 microgram is the upper limit
(B) 0.5 microgram DNA / 5kb DS plasmid + 3.2 pmol primer in 13 microliter, 2 micrograms is the upper limit
(C) 100ng / 1000bp PCR + 0.8 pmol primer in 13 microliter
 
What should the melting temperature of my primers be?
The Tm should be in the range: 52º-60º C.
 
How should I label and name my samples?
We ask that your sample names be no longer than six spaces. Within the six spaces, your labels can use any letter and the following punctuation only: -_(){}#.+. We also ask that you write your sample names on the TOP of the tube.

If we receive samples with very long names, we may assign a new name to each sample consisting of your initials and a number. If you would like to keep track of your samples with a longer name, write your own name on the side of your tube. Just as long as a simple labeling system is on the TOP of the tube, and it matches your order form. Thanks.
 
How much does it cost?
$5.00 per sample for UC labs, $5.15 for LBNL affiliated labs, and $7.65 for outside organizations regardless of the result, so it is in the user's interest to supply clean DNA.
 

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