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sonication for ChIP


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3 replies to this topic

#1 ti2004

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Posted 01 November 2004 - 02:12 AM

Hy!

I would like to sonicate eukaryotic cells in order to perform chromatin immunoprecipitation. Our sonicator is a warter bath- sonicator. Regulation of the amplitude or any other parameters is not possible. I can set only the time of the sonication (not the rests between them). I would like to receive advises about sonication protocols for ChIP with sonicators of that type. Thank you!

ti

#2 pcrman

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Posted 01 November 2004 - 04:06 PM

Hi,

I have not worked with that type of sonicator. However, no matter what machine you use, you should run a preliminary experiment to determine the optimal condition. You can use the same number of cells you would use for formal experiment and do the sonication with different settings, then reverse crosslink the DNA, phenol/chloroform purify it and run a gel to see which setting give the best result.

During the sonication, keep your sample in a ice-water bath to reduce heat.

#3 sonix82

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Posted 12 November 2004 - 06:37 AM

Hi,

The sonicator you have is mainly used for cleaning. It will most likely not be strong enough to shear DNA to the base pair range you need. If you find that this is the case, you may want to check out actual sonicators as opposed to ultrasonic cleaning baths. The following is a link to Misonix, who sells sonicators for this application and can provide a lot of support for doing ChIP assay.

http://www.misonix.com/

#4 Hielscher_Ultrasonics

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Posted 23 November 2009 - 08:05 AM

Hy!

I would like to sonicate eukaryotic cells in order to perform chromatin immunoprecipitation. Our sonicator is a warter bath- sonicator. Regulation of the amplitude or any other parameters is not possible. I can set only the time of the sonication (not the rests between them). I would like to receive advises about sonication protocols for ChIP with sonicators of that type. Thank you!

ti


Hi ti2004,

an ultrasonic cleaning tank is nice for cleaning but not very effective for ChIP. This is due to the very limited amplitude and distance between actuators and your sample.

You may want to have a look at our following products:

VialTweeter - Intensive Sonication Small Volumes

UIP250MTP - Sonication of Microtiter Plates

Have a nice day!




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