Information about Available KO Strains

Updated August.10.2007

 

Please note the following regarding annotation changes:

 

• To find out exactly what was deleted, search the genome with primers 5r and 3f – the region between them was deleted and replaced with the hph cassette for a given gene.
• Some NCU numbers have the suffix .1 – this means that the primers used to knock out these genes were based on the earliest annotation.  The region deleted may not correspond correctly to the ORF when the later annotations are considered.  (Note that some .1 NCU numbers no longer exist as a .2 or .3 version.) 
• However, if you look up NCU numbers in our LIMS, you must use a .2 suffix.
• A few genes were knocked out in both their .1 and .2 versions.
• Most of the primers used are based on the .2 annotations and we have retained this suffix, even if the .3 version is UNCHANGED.
• However, we have included a column listing the Broad’s designation for the differences between the .2 and .3 versions for your information.  Many that are CHANGED are different from .2 in ways that will not affect whether the ORF was properly knocked out.  Please evaluate your knockouts of interest by locating primers 5r and 3f on the sequence, as mentioned above.

 

Notes about strain validation:

 

• All homokaryotic strains have been validated by Southern analysis. 
• Most heterokaryotic knockouts have been validated by Southern analysis. Some of the earliest heterokaryons submitted have not yet been subjected to Southern analysis, as noted.
• For most of the first 2,500 or so genes we have used the entire cassette as the probe – this approach ensures strain identity, lack of ectopic insertion of any portion of the transformation cassette, and lack of contamination of the homokaryotic KO strain by wild type.
• However, we have observed that the frequency of ectopic insertions or wild-type contamination has been extremely low.  Therefore, we have changed our procedures such that we now use only the hph cassette as the Southern probe.
• Blank entries are in the process of being updated.