Hi everyone,
This may be a really silly question, but why do we need to size-select the ChIP sample before PCR amplification? To me it makes more sense to keep as many molecules of the sample and amplify those, rather than limit the material by size selecting it.
I have tried out both, and although I get much more material of a tighter size range with a size selection step before PCR, I can also produce a library with a wider size range (but less DNA) without this step. At least this is what the bioanalyzer results tell me - I haven't sequenced them.
I am using 1xAMPure beads after adapter ligation, and expect them to get rid of my adapters.
Is there a flaw in my thinking? I hope somebody out there can share their experience with me.
Thanks!
Maike
This may be a really silly question, but why do we need to size-select the ChIP sample before PCR amplification? To me it makes more sense to keep as many molecules of the sample and amplify those, rather than limit the material by size selecting it.
I have tried out both, and although I get much more material of a tighter size range with a size selection step before PCR, I can also produce a library with a wider size range (but less DNA) without this step. At least this is what the bioanalyzer results tell me - I haven't sequenced them.
I am using 1xAMPure beads after adapter ligation, and expect them to get rid of my adapters.
Is there a flaw in my thinking? I hope somebody out there can share their experience with me.
Thanks!
Maike
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