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Old 09-16-2010, 10:23 AM   #3
Location: San Diego

Join Date: Sep 2010
Posts: 26

Originally Posted by superduper View Post
Hi clpX,
Could you share the protocol you used for ChIP-library preparation? I am have some trouble with my ChIP-libraries. The main failure in my prep is that I do not get amplification after size selection. I could actually see DNA on the gel when I cut out the 180-300 bp slice. However, after PCR all I got was just primer dimer that migrates way below 100 bp.
I would double check your primers compared to what you are putting on as adapters. If you have material, but you cannot amplify it...there is a simple reason.

1. Primers do not match/hybridize to target DNA...why this is happening is the game you will have to play. Either primers or adapters. Do you run a positive control for your PCR reactions? You should. Could be your Master Mix too.
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