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Old 10-05-2011, 09:34 AM   #1
jazz
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Default ChIP-seq DNA concentration

Hi everyone,
I am doing a ChIP-seq using Illumina platform. After IP, I have less than 10 ng of DNA, while I have at least 10-fold excess in Input. My question is whether it is important to use same amount of Input and ChIP DNA before library preparation. The reason I am worried about this is 2-fold
a) If using different IP and input DNA before library prep, how else is the data normalized?
b) If starting with different amounts of DNA in the final PCR amplification step, there could be a differential amplification of some regions, skewing the data.

What are your thoughts.
Thanks for all inputs.
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Old 10-07-2011, 07:16 AM   #2
kthai
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Yes, I completely agree with you. When I prepare my ChIP-Seq libraries, the input and IP concentrations are the same to reduce any biases, especially during the amplification stage.
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