Information about Available KO Strains
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
cassette for a given gene.
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
(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,
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
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
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
cassette as the Southern probe.
Blank entries are in the process of being