AFLPs - few bands in AFLPs (Jul/19/2005 )
I’m working with AFLPs and I had already quite good results at the beginning of my work but after about twenty samples (with different primers) there came out only a few peaks at the beginning! I suppose there could be a problem with the restriction-ligation because I’ve tried to control the different steps of the AFLPs, doing parallel preparations with samples that have already worked and therefore I think the problem has to be in the first step! I’ve changed all my reagents with new ones but there was no improvement! Can anyone give me some good advice or did anybody have the same problems?
I too am having similar problems and have been trying to debug it. I am not sure but you can try a test digestion and run it on an agarose gel to see if that is the step that's going wrong. For me, the digestion seemed to work well, but I couldn't figure out how to test the ligation since it gives the same sort of gel pic as the digested ones on an agarose gel.
I use Licor-IR 700 dye kit and have been able to get some bands with the control pre-amplification DNA that they send but for the DNA I wish to, I had no luck. I am trying it with C elegans DNA. Just curious, what genomic DNA do you use?
Would be grateful if someone can help us out or provide some suggestions.
I'm working with genomic DNA from Astacus astacus (noble crayfish) - but I don't have an AFLP - Kit so I have no possibility to control my own samples. I have only the samples that have already worked but unfortunately the other samples aren't working at all (always following the same protocol)!