I am trying to find a good negative control gRNA in my experimental system. I found that Zhang laboratory provides sequences of non-targeting gRNA in their gRNA libraries, some of which are used as negative controls in papers published from other laboratories. I understand that I need to check which non-targeting gRNA works as a negative control in the cell lines I use, but I want to narrow down the candidates by computationally predict off-target effects. Is there any good tool to predict the off-target effect of an already designed gRNA?
Dear Tomohiro,
one possibility would be to use a gRNA design tool as for instance CC-Top (https://crispr.cos.uni-heidelberg.de/).
As a query sequence, you can past your already designed gRNA sequence (containing the PAM-sequence!), choose the PAM type and species.
This leads to a table, which, besides your target, includes possible off-targets.
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