So,
Long story short, our collection of mutants got their labels mixed up, and now I need to identify the site of mutations. This collection of flys was a mishmash of various P-elements - aka pBac, P{XP} Mi{ET} etc.
I've tried internal PCR using pBac and p{XP} primers, but have come up fairly empty handed.
Part of the problem is that we have a lot of random DNA floating around in the lab, and with 40 x 2 PCR amplifications of the nested PCR along with the sequencing reaction, I'm not sure that I'm not amplifying random tidbits that are floating around.
I would like to restart with the genomic prep of the flies, and then try to identify the type of P-element first before proceeding to PCR/sequencing.
Are there any good ways of going about doing this?
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