Background

CRISPR/Cas9 is the current technology of choice for genome editing. This is due to its versatility, as it is an RNA guided system where a 20-base crRNA and a tracrRNA (together called a guide RNA - sgRNA) direct a Cas9 nuclease (from Streptococcus pyogenes) to the target sequence providing high specificity with minimal secondary site effects. At the target site the endonuclease makes a double-stand cut of the DNA, which can then be resolved through Non-Homologous End Joining (NHEJ) or Homology Dependent Repair (HDR). CRISPR-Cas9 technology was first adapted for C. elegans in 2013 and since then the community has produced increasingly more sophisticated methods to mutate, delete and tag genes. These approached have included Cas9 variants with different protospacer-adjacent motifs (PAM sites).
At this site we use current (as of March 2016) best practices to identify potential guide RNAs for the entire C. elegans genome.

Guide design

The following steps were taken to design the guides present in the database. The calculations were performed with an in-house Perl script/wrapper using the genome sequence and gene annotation obtained from WormBase version WS250.

For questions concerning CRISPR/Cas9 and the role of this methodology in the goals of the C. elegans knockout facility contact Don Moerman. For more specific questions concerning parameters and filters used to choose the guide RNAs contact Stephane Flibotte.

How to view the guides in the integrative genomics viewer (IGV)

All guides are listed in a text format with their coordinates on the chromosome along with a listing of what gene feature they affect. For those who would like a more visual view of this information we suggest they use the following. All the guides passing the default filters are available for bulk download in bed format. Follow these instructions to view the data in IGV, the Integrative Genomics Viewer from the Broad Institute:

Additional C. elegans databases hosted here