1 reply to this topic

[MJH]

Hi everyone,

I am a newby to chIP and have one question that I haven't been able to find an answer to and another that I haven't found a definitive answer to.

First: What is the common procedure for cleaning the sonicator tip before and between samples to prevent DNA contamination of the chromatin preps? Based on basic organic chemistry, I'm leaning toward a 5 minute soak in 10% bleach followed by 3 70% ETOH washes.

Second: Our lab has an Aquasonic water bath sonicator (model 150D) that I would like to use to shear my chromatin preps as it solves the issue of DNA contamination via the sonicator tip, allows me to shear multiple samples at once and prevents aerosolization of the samples. However, based on everything I've read, I'm concerned that the Aquasonic would not produce the frequency of sonication necessary to shear the DNA (the manual says it produces 50-60 Hz).

If anyone has used this model of sonicator (or something comparable) to successfully shear chromatin I would be very happy if you would share your protocol with me.

Many thanks in advance,
MJH

[laurequillo]

MJH, on Feb 23 2010, 08:38 PM, said:

Hi everyone,

I am a newby to chIP and have one question that I haven't been able to find an answer to and another that I haven't found a definitive answer to.

First: What is the common procedure for cleaning the sonicator tip before and between samples to prevent DNA contamination of the chromatin preps? Based on basic organic chemistry, I'm leaning toward a 5 minute soak in 10% bleach followed by 3 70% ETOH washes.

Second: Our lab has an Aquasonic water bath sonicator (model 150D) that I would like to use to shear my chromatin preps as it solves the issue of DNA contamination via the sonicator tip, allows me to shear multiple samples at once and prevents aerosolization of the samples. However, based on everything I've read, I'm concerned that the Aquasonic would not produce the frequency of sonication necessary to shear the DNA (the manual says it produces 50-60 Hz).

If anyone has used this model of sonicator (or something comparable) to successfully shear chromatin I would be very happy if you would share your protocol with me.

Many thanks in advance,
MJH

I just clean the tip once with ethanol 70% before and between samples. You can add a extra wash between samples with lysis buffer. I had no contamination problems.

I tried a water bath sonicator once but I dont remember the brand. They brought the sonicator to my lab and we did some test with it. It worked quite well

Edited by laurequillo, 23 February 2010 - 12:51 PM.