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RNase treatment before analyzing sonicated chromatin in ChIP


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#1 Juni

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Posted 21 October 2009 - 08:31 AM

Dear All,
I just entered in the world of ChIP, and I am currently the only one in my lab to dare starting with this technique.
My question is:
After sonication, I wanted to see the DNA fragments range on agarose gel. So I run the RNase-untreated and RNase-treated DNA sample on 1% agarose gel.
I got one thick band in the lane where I did not add the RNase (no visible smear) while a small smear in the lane where I added RNase (thick band disappeared).
Is this thick band correspond to RNA presence?
I am unable to interpret this for the moment.
If any of you could help me, please
thanx
Juni

#2 Clare

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Posted 22 October 2009 - 01:51 AM

Dear All,
I just entered in the world of ChIP, and I am currently the only one in my lab to dare starting with this technique.
My question is:
After sonication, I wanted to see the DNA fragments range on agarose gel. So I run the RNase-untreated and RNase-treated DNA sample on 1% agarose gel.
I got one thick band in the lane where I did not add the RNase (no visible smear) while a small smear in the lane where I added RNase (thick band disappeared).
Is this thick band correspond to RNA presence?
I am unable to interpret this for the moment.
If any of you could help me, please
thanx
Juni


Most likely, yes <_< Your DNA should look like a smear after you treat with RNase :blink:

Clare

#3 Juni

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Posted 23 October 2009 - 01:10 AM

thanks Clare for your reply,
juni




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