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Deletion strains originating in the Vancouver Gene Knockout Lab (with a VC strain name) are stabilized lines. Each line is either homozygous for a deletion or heterozygous for a deletion and a genetic balancer. The strains may carry alleles generated either in the Vancouver lab (with gk designations) or alleles generated in the Oklahoma lab (with ok designations). Detailed information about a strain, including genotype, phenotype, deletion breakpoints, deletion size, and primer sequences, can be found in its corresponding on-line strain sheet, which is generally accessible from the strain list at the Caenorhabditis Genetics Center.
The deletions carried by these strains are detectable by nested PCR using the primer sequences on the strain sheet. In most cases, only the mutant product is seen in reactions from balanced heterozygotes, so presence of the wild-type band should not be used as an indicator of heterozygosity in subsequent outcrosses. Single-round PCR using individual external or internal primer pairs may also yield detectable amounts of product, but we do not routinely perform such reactions. Our standard PCR protocol can be found at http://ko.cigenomics.bc.ca/knockout3.html. Deletion breakpoints and presence of any insertions or islands of DNA are determined by DNA sequencing from PCR products, followed by a BLAST search of the C. elegans sequence database and/or sequence comparison within ACeDB. Breakpoints are given as numerical ACeDB cosmid coordinates, corresponding to the bases flanking the deletion, and as actual sequence. In cases where breakpoints are ambiguous, the range of possible positions for the break in the ACeDB sequence display is given, and the ambiguous portion is set between slashes. Any phenotype described for deletion homozygotes has segregated with the deletion through sib selection, but since the mutation has been outcrossed only minimally, the phenotype may not be a consequence of the deletion. You may want to outcross the strain more extensively prior to any further characterization. Finally, you should be aware that the deletion may be accompanied by more complex rearrangement of the genome, and that the lesion may not be a null. We and Caenorhabditis Genetics Center would appreciate receiving any data you collect bearing on these points. Deletion strains are provided as-is and free of charge by the International C. elegans Gene Knockout Consortium (http://www.celeganskoconsortium.omrf.org/). Please acknowledge our contribution in any publications or communications resulting from use of this mutation with the following statement, and forward 2 copies of the reprints to us (PDF files are fine): |
| "Some deletion mutations used in this work were provided by the International C. elegans Gene Knockout Consortium (C. elegans Gene Knockout Facility at the Oklahoma Medical Research Foundation, which is funded by the National Institutes of Health; and the C. elegans Reverse Genetics Core Facility at the University of British Columbia, which is funded by the Canadian Institute for Health Research, Genome Canada, Genome B.C., the Michael Smith Foundation, and the National Institutes of Health)." |
