2 replies to this topic

[rahulr1485]

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?


ChIP DNA Sample


Input DNA

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

[pcrman]

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

[rahulr1485]

pcrman, on 01 June 2011 - 09:08 PM, said:

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.