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C. elegans Fosmid Library

C. elegans Fosmid Library

The availability of genomic clones with 35 to 40kb inserts has been a critical resource to the C. elegans community. Fingerprinted and ordered cosmid clones harboring such inserts were the backbone of the sequencing project. Further utility was found, when individual research labs were trying to map mutants. Complementing a mutant by injecting a strain with overlapping cosmid clones eventually led to mutation identity. This approach is still widely used and is an important tool for mutational analysis. Many of the cosmid libraries are now 20 years old and there are reports of some of them losing viability.

With these considerations in mind Don Moerman et al have chosen to make a fosmid rather than a cosmid library. The library was constructed using the fosmid vector pCC1FOS (Epicentre) and is maintained at low copy number until induced. The use of fosmids as backbones allows for the maintenance of large pieces of DNA (around 40kB) in limited number (1-5) per bacterial host. Up to this point, such a resource was unavailable for C. elegans.

The N2 fosmid clones are mapped to the C. elegans genome by pair-wise alignment of fosmid end-reads. Initial analysis of the library quality shows that the average insert size is ~ 43,284 bp and 86.7% of the clones have paired end-reads with correct relative orientation. The library obtained approximately 5.74X clone coverage of the genome.

This resource was presented at the Fifteenth International C. elegans meeting.

41 x 384 plates with a total of 15,744 clones.

Protocols / Clone Handling

Please note that the clone(s) are tested as negative in our phage contamination assay prior to shipping. However, these clones should still be handled with care as no phage assay can be guaranteed to be 100% accurate.

Plates: contain LB broth with 8% glycerol and chloramphenicol. These are sent on Dry Ice. These should be stored at -70°C.

Clones: are streaked onto LB agar containing chloramphenicol (12.5µg/ml).

To use: re-streak the clone onto the same agar type, in such a way as to obtain single colonies. Incubate at 37°C overnight. Clones can be grown in LB broth + chloramphenicol, and glycerol added after growth to a concentration of 25% for long-term storage at -70°C.

These clones are for research purposes only.

References

Jaryn Perkins1,2, Kim Wong3, René Warren3, Jacquie Schein3, Jeff Stott3, Rob Holt3, Steve Jones3, Marco Marra3, and Don Moerman1,2

  • 1Michael Smith Laboratories, U.B.C., Vancouver, B.C., Canada V6T 1Z4

  • 2Department of Zoology, University of British Columbia, B.C. Vancouver, Canada V6T 1Z4

  • 3Genome Sciences Centre, BC Cancer Agency, Vancouver, B.C. Canada, V5Z 4S6


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