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ChIP- Different DNA size for Input DNA and ChIP DNA on Agilent Bioanalyzer


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#1 rahulr1485

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Posted 01 June 2011 - 07:46 AM

I ran one of my input DNA and all my ChIPd DNA on Agilent Bioanalyzer today.And I am getting different DNA sizes for my input and ChIP DNA samples.Input shows a distribution around 100-300bp while ChIp samples is distributed around 900-6000bp. I processed them together ,decrosslinked overnight and cleaned up using Qiagen PCR clean up kit. I diluted the input 360 X to get 100pg/microlitre and the ChIPd DNA samples 10X to 300-500pg/microlitre before running on the Bioanalyzer. I am using Agilent High Sensitivity kit which expired on 3rd May 2011. The ladder ran correctly. So I am not sure if this inconsistency is due to the kit.
What could be the reason for this difference?

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ChIP DNA Sample

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Input DNA

Edited by rahulr1485, 01 June 2011 - 08:55 AM.


#2 pcrman

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Posted 01 June 2011 - 09:08 PM

This is weird. It seems that something in the ChIP DNA sample such as protein is affecting DNA migration.

#3 rahulr1485

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Posted 03 June 2011 - 03:50 AM

This is weird. It seems that something in the ChIP DNA sample such as protein is affecting DNA migration.

Thank you for the reply. I treated it with Proteinase K and cleaned up with Qiagen Kit. But it still looks the same.




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