Will salmon sperm DNA in ChIP protocol interfere the WGA amplification? - (Dec/21/2008 )
Hi All,
Routinely in ChIP protocol, we use sonicated salmon sperm DNA to incubate with protein A/G in order to reduce unspecific binding. This salmon sperm DNA will end up present in the final ChIPed DNA. If someone is going to perform ChIP on chip and need to amplify the ChIP DNA, will this salmon sperm DNA be amplied as well? Also if someone measure the final amount of ChIPed DNA which will not be correct if there is salmon sperm DNA present. Dose anyone of you in your ChIP protocol not include this salmon sperm DNA ? Thanks
-hkwong-
QUOTE (hkwong @ Dec 22 2008, 06:15 AM)
Hi All,
Routinely in ChIP protocol, we use sonicated salmon sperm DNA to incubate with protein A/G in order to reduce unspecific binding. This salmon sperm DNA will end up present in the final ChIPed DNA. If someone is going to perform ChIP on chip and need to amplify the ChIP DNA, will this salmon sperm DNA be amplied as well? Also if someone measure the final amount of ChIPed DNA which will not be correct if there is salmon sperm DNA present. Dose anyone of you in your ChIP protocol not include this salmon sperm DNA ? Thanks
Routinely in ChIP protocol, we use sonicated salmon sperm DNA to incubate with protein A/G in order to reduce unspecific binding. This salmon sperm DNA will end up present in the final ChIPed DNA. If someone is going to perform ChIP on chip and need to amplify the ChIP DNA, will this salmon sperm DNA be amplied as well? Also if someone measure the final amount of ChIPed DNA which will not be correct if there is salmon sperm DNA present. Dose anyone of you in your ChIP protocol not include this salmon sperm DNA ? Thanks
We use ssDNA, but only in the pre-clearing step.
Clare
-Clare-