I have been trying to perform the control template for 3C assay which consists of amplifying from the gDNA small fragments ( your controls) purify from the gel, put them together in equimolar concentration, digest and ligate (to get all the possible combinations).
After that I'm supposed to performe a standard curve using this DNA template to check the primer efficiency.
The thing is: for the standard curve the first dilution has a low ct ( around 20) and the second ( 10x) goes to 32, the third goes to around 34 and the forth and fifth do not amplify. I repeated many times and got the same pattern. I started with more diluted dna, but then I get amplification just in the first cycles and sometimes the second dilution gives me a lower CT value than the first.
The only thing i did different from my collegue ( that has it working) was the ligation step. I did in a larger volume ( of course adjusting all the reagents), but the DNA was in a lower concentration compared to my colegue. Does it make a difference? Does it explain this weird result from the aplification for standard curve?
Thanks a lot.