I have a quick question regarding the impact of GC representation in my sample preps. I am looking at different sample prep kits to use and one has slightly higher GC representation (upwards of 50% with 10% variability). Is there a ceiling that I would run into limitations in my results because of this? A colleague has raised significant concern that this is an issue but I do not see an issue as long as the variation is predictable and in a narrow range.
Does anyone have any thoughts on this? Thanks a lot.
I don't see why it would be a problem. If you're enriching you might have to fiddle with the pcr conditions.
If it does not exceeds 80% ( a unique sample from a unique organism ) no problem.
Thank you everyone for your help. If you come up with any other thoughts let me know, but I think I can move forward pretty comfortably.
GC percent is only a guideline and one can use varying percentages and be satisfied if the amplification occurs and the primer-dimer problem is not enormous
yeah, I am trying to push to low level of inputs in the picogram range and the GC issue arose. it is predictable and with little variability from run to run. Siva, you highlight an interesting point about the primer-dimer problem, and that is part of what I am seeing. It is limited though and the other results look great. I appreciate the insights.
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