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Sonication's fault or gel's fault?

Sonication's fault or gel's fault? - ChIP Chromatin Immunoprecipitation Forum

Sonication's fault or gel's fault? - Chromatin Immunoprecipitation Forum. Discuss, chat about, and post questions about the ChIP assay, in the ChIP forum. Includes troubleshooting, protocols, buffer preparation, and more.


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Old 12-13-2012, 03:49 AM
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Default Sonication's fault or gel's fault?



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 Images
File Type: jpg running gel.jpg (23.4 KB, 3 views)
File Type: jpg 2012-12-03 14hr 26min-3990.jpg (14.8 KB, 2 views)
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