Conditional Knockout

I require a cell-specific knockout mutant, and to me it seems the best way to go about this is using Cre/loxP or FLP/FRT. I was wondering whether
anyone had any advice as to which of the two works best in C. elegans for this application? And whether this is the best way to go about
creating a cell-specific knockout in the first place?

I believe both have been used successfully (I think FLP more, or more recently?), and in theory either should work.

You could also try expressing a hairpin RNAi construct. It’s not a good method, at all, but: it’s incredibly easy! It might offer you encouragement to do the harder work of getting the absolute certainty from Cre/Lox or FLP/FRT.

FLP/Frt and Cre/lox systems have both been shown to work quite well. We generated a series of stable and efficient tissue-specific FLP lines that potentially could be useful to you:
plus a few newer ones (contact us if you are interested).

Keep in mind that protein stability will influence how fast a potential phenotype appears. The FLP/Frt and Cre/lox systems will knock out your gene but existing protein might still be around for a while, at least in non-dividing cells. Targeted protein degradation systems (e.g. PMID: 26552885; PMID: 28619826) are attractive alternatives that can be used alone or in combination with either FLP/Frt or Cre/lox to ensure maximum phenotypes. In our hands the protein degradation systems are efficient, but they don’t deplete our target proteins completely so the combination can be useful.

Good luck!