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Dirty precipitates after sonication


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4 replies to this topic

#1 TracyDuke

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Posted 16 July 2009 - 02:04 PM

Hi All, I used to be able to have cells well sonicated in 1 ml solution. I am currently trying to do ChIP with less amount of cells hence in less volume solution (300 ul). I found the lysates get really dirty after sonication with dark precipitates. Why is that?

#2 cellcounter

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Posted 19 July 2009 - 02:16 PM

Hi All, I used to be able to have cells well sonicated in 1 ml solution. I am currently trying to do ChIP with less amount of cells hence in less volume solution (300 ul). I found the lysates get really dirty after sonication with dark precipitates. Why is that?

More information on cell type and machine you are using may be helpful.

#3 Radish

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Posted 21 November 2009 - 05:54 PM

Hi All, I used to be able to have cells well sonicated in 1 ml solution. I am currently trying to do ChIP with less amount of cells hence in less volume solution (300 ul). I found the lysates get really dirty after sonication with dark precipitates. Why is that?

Lately I am having the same problem :D

In my case I am using a bioruptor 200, E14 cell line and they are being sonicated in 1 ml.

When I centrifuge the lysates after the sonication it looks like a thread, with brownish/black color.

Thank you very much in advance.

#4 KPDE

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Posted 22 November 2009 - 10:08 AM

Hi All, I used to be able to have cells well sonicated in 1 ml solution. I am currently trying to do ChIP with less amount of cells hence in less volume solution (300 ul). I found the lysates get really dirty after sonication with dark precipitates. Why is that?

Lately I am having the same problem :huh:

In my case I am using a bioruptor 200, E14 cell line and they are being sonicated in 1 ml.

When I centrifuge the lysates after the sonication it looks like a thread, with brownish/black color.

Thank you very much in advance.


Interesting. I used to use a Misonix 3000 with a microtip and got what you're describing and then switched to using a Bioruptor and the dark precipitate went away. In any case, I haven't seen much of a difference in yield or enrichment between when I was getting the precipitate and when it went away.

#5 Radish

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Posted 22 November 2009 - 04:04 PM

Hi All, I used to be able to have cells well sonicated in 1 ml solution. I am currently trying to do ChIP with less amount of cells hence in less volume solution (300 ul). I found the lysates get really dirty after sonication with dark precipitates. Why is that?

Lately I am having the same problem :huh:

In my case I am using a bioruptor 200, E14 cell line and they are being sonicated in 1 ml.

When I centrifuge the lysates after the sonication it looks like a thread, with brownish/black color.

Thank you very much in advance.


Interesting. I used to use a Misonix 3000 with a microtip and got what you're describing and then switched to using a Bioruptor and the dark precipitate went away. In any case, I haven't seen much of a difference in yield or enrichment between when I was getting the precipitate and when it went away.

I have been furiously trying to get into the fast-ChIP protocol and I can't even get passed the sonication.
Everything always goes completely wrong.
LOL the only way to alleviate my failure is to laugh :D


Thank you so much for the feedback, at least this way I Know the it is not an unseen thing.

Edited by Radish, 22 November 2009 - 04:27 PM.





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