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Sonication's fault or gel's fault? Help please!


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#1 ChIP Kick

ChIP Kick

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Posted 12 December 2012 - 12:51 PM

Hi guys,

I have some problems with my ChIP assay. Hope you can give me some suggestions.

I sheared some formaldehyde cross-linked tissues samples. Then, treated with RNase A at 37C for 30min. After adding protinase K, reversed crosslinking at 62C for 2hours. Then run a 1% agarose gel with 85voltage.

Here are the problems. I do not know why there are red lines(in attached file) in my gel when running? In gel images, why I do not have smeared DNA?

My sonicator is Qsonics Q125. Sonication with 30% power, 15sec on, 45sec off, 10cycyles.

Is there someone can help me? Thank you very much!

Attached Thumbnails

  • running gel.jpg
  • 2012-12-03 14hr 26min-3990.jpg





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