Originally posted by ashchin
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I started off fragmentation with 2.4 ug (calculated by QuBit BR) in 120 ul and then purified with AMPure beads. Then, remeasured the concentration with QuBit HS and got 50ng/ul as the Truseq protocol recommends.
I've tried different ligation time and also different PCR input several times. Different from the previous PE protocol, longer ligation time resulted in dimer issue. Also, too much PCR input did too. I strictly keep 10 minute ligation time and then put stop ligation buffer and also used 3-4 ng of input for amplficiatoin, which I am a bit worried about library complexity.
Anyway, it might be interesting to sequence dimer library and non-dimer library.
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