I am working to make some small RNA sequencing libraries, and have just started using real time PCR to quantify them. The final steps of my library construction are to do 12 PCR cycles, then gel purify. On the gel, all my samples looked to be approximately the same concentration. I cut out the desired size, soaked & purified, and finished with PCR quantification (I'm using KAPA, if it matters). The qPCR results varied very widely from a low of 0.44 pM to a high of 1600 pM, both of which are within in the range of the standard curve.
So...
1. Should I proceed with sequencing samples below a certain concentration? And do people have a lower cut-off they think is acceptable?
2. Can I just do more PCR with the samples that are low? And is there a limit for how many additional cycles I should do?
So...
1. Should I proceed with sequencing samples below a certain concentration? And do people have a lower cut-off they think is acceptable?
2. Can I just do more PCR with the samples that are low? And is there a limit for how many additional cycles I should do?