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Each cell line is designated by a two- or three-letter prefix followed by three numbers. For example, a valid cell line name is XB003, but not XB3.
Control samples are designated by the prefix "ZZ" (e.g., ZZ001, ZZ202). Control samples are ignored by subsequent data processing.
To automate the data processing, the finished ABI trace files follow a specific naming convention. The cell line name appears first, followed by the primer code for the vector, followed by any additional alphanumeric groups (e.g., sample location on the PCR plate). A single underscore separates each group -- not a space, hyphen, or any other character. There can be no spaces anywhere in the file name.
Prior to sequencing, e-mail the primercode and associated vector name to Doug Stryke at stryke@cgl.ucsf.edu. Note that once established, the vector designation for a primer code cannot change. E-mail new vector sequences to michiko@cgl.ucsf.edu.
Within file names, cell line names may contain a letter suffix (e.g., XB006A) for experimental purposes. However, these suffixes will not be part of the final cell line name and will be removed during subsequent data processing. Also, no two files in a batch can refer to the same cell line (again, regardless of any suffix).
If a validly named sample refers to a cell line already in the database (regardless of any suffix), it will be rejected. The existing cell line will remain in the database and on the web site. This means that existing cell lines must be removed prior to submitting replacements. In the unusual event that existing cell lines must be removed, email your request, a list of the cell line names, and the reason for their removal to Doug Stryke at stryke@cgl.ucsf.edu.
When sending a sample request sheet to the UCSF Genomics Core Facility, whether for new PGA sequences or for existing sequences that now should be part of the PGA database, designate in the request e-mail that the data be placed in the PGA folder.
If a sequence that was not designated for the PGA folder is to replace a previously entered cell line in the PGA database, then a request will have to be made to the GCF to move the file from the MAC or PC folder into the PGA folder. Only the GCF has access to move trace files and ABI data from one folder to another.
Last updated 19 Apr 2005.