NIA Clone Set Rearray Help File

Clone Names and Verification of NIA cDNA Clone Identity

Parental clone names identify clones from the originally derived NIA cDNA libraries. These clones are sequenced from both 5.- and 3.-ends (read 1). Based on these sequence information, non-redundant cDNA clones are selected. Selected clones are re-arrayed (picked from parental stock plates and arranged in a condensed collection on new plates). Clones re-arrayed in this way are called daughter clones. To help protect against contaminants, some collections go through an additional round of single colony isolation, where re-arrayed clones are grown on plates and single colonies from these plates are selected for a copy of the re-array. When daughter sequences of the copied re-array (sequence read 3) match parental sequences (sequence read 1), the identity of the clone has been preserved (i.e. there was no error in re-arraying the clone during the entire process), and the clone is said to be verified. Alternatively, if a phase 2 daughter clone sequence (sequence read 3) fails to match the parental sequence, the phase 2 daughter sequence is then compared to the phase 1 daughter sequence (sequence read 2).

If these two daughter sequences match (but fail to match the parental sequence), the clone is verified but dubbed an orphan clone to distinguish it from those clones matching their respective parents. Clones from daughter clone collections phases 1 and 2, together with the clones from the parental libraries, will all have unique clones names even though they generally belong to the same clone lineage. Unique names are necessary for database record keeping and because the supposed identity of clones must be verified every time they are re-arrayed.

Naming Conventions

Clone Names: All NIA cDNA clones, including ones that had been done in our laboratory before moving to NIA, have been named in the following manner. As an example of NIA naming conventions, a parental clone might be named J0054A09, the phase 1 daughter might be called something like H8035D07, and the phase 2 daughter might be called H4035D07. The first part of the name (one letter and four digits), in this example J0054, H8035, and H4035, respectively, gives the serial number of the plate where the clone can be found. This final part of the name (one letter and two digits), in this example A09, D07, and D07, respectively, gives the well position of the clone in the plate.

Sequence Names: Sequences obtained from the 5.-end of cDNA clone (e.g., H3078A10) are named with .-5. (e.g., H3078A10-5), whereas the sequences obtained from the 3.-end of cDNA clone are named with .-3. (e.g., H3078A10-3). When these two sequences were overlapped and assembled by Phred/Phrap, the assembled sequences are named with .-0. (e.g., H3078A10-0).

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