Primer Database

The primer database is a growing list of the various primers used and owned by the Barrick Lab. When new primers are bought, they should be entered into the database, and when a specific primer is needed, looking it up in the database can prevent an unnecessary purchase.

Entering Primers

Go to the lab database and select primers, followed by insert.

First of all, enter the initial and number of the primers into the corresponding fields.

For box number, state in which box in the -20°C freezer the primer are or will be located.

For project, name the project for which these primer were ordered.

For gene, list the genes relevant to this primer. For instance, if this primer covers all of gene abcD and no other genes, write abcD. If this primer covers only part of abcD, write [abcD]. If this primer covers the noncoding region inbetween abcD and efgH, write abcD/efgH. If this primer covers the all of abcD and some of efgH, write abcD, [efgH].

For template, write the strain for which this primer was designed. It is often more useful to write the ancestor of the actual strain (for instance, a primer which was made for a descendent of REL 606 would still have only the ancestor listed).

For start and end, write the positions for the first and last bases, respectively, of the primer, remembering to follow the 3' to 5' notation. Thus, for a forward primer, end > start, but for reverse primers, start > end.

For sequence, write the actual sequence of the primer 3' to 5'. For the sequence and start/end, it is advisable to copy and paste the entries to avoid typos which occur very easily when writing long strings of numbers or letters.

For description, give a short description of what purpose the primer serves in the project. Ex: F primer for identifying mutations in abcD in strain 777.

Lastly, enter the date on which the primer was ordered, check over the data entries and hit go to enter the primer into the database.

Remember that primers can be updated anytime, and it may be necessary to do so if the primer is moved to a different location that where it was originally placed.

Searching for Primers

Go to the lab database and select primers, followed by search.

The most common use of the search feature is to locate primers that have already been ordered and received. To do so, searching by initial and number should locate that primer.

However, searches can also be used to check if a desired primer is already in the lab, and if so, where it is located. Most likely, this would be done by searching for a specific sequence, or at least a sufficiently similar sequence (sequences similar but not the same can be found by selecting "Like %...%" in the operator column) to the one needed. Alternatively, the the location (start/stop points) and the genes copied can also be used to search for primers, but these less likely to be successful.

In all cases, make sure that the template of the newfound primer matches the organism from which the DNA will come.

Contributors

Aurko Dasgupta, Jeffrey Barrick