Hi,
I'm having issues with finding the best protocol to check the size of sonicated fragments from my chIP samples.
Most protocols recommend just reverse-crosslinking a subset of the sonicated material and then running it on an agarose gel. This is what I have been doing to date, however, I think what I have been visualising is mostly RNA not DNA.
So, I have recently tried preparing them the same as I would my INPUT samples (RNase A treated, then Proteinase K treated, Reverse-crosslinked, P:C:Ia cleaned, etc) and run the cleaned products on a gel. After this thorough process I have no DNA product on my gel.
Can anyone suggest a 'standard' procedure that everyone should be following?
I'm having issues with finding the best protocol to check the size of sonicated fragments from my chIP samples.
Most protocols recommend just reverse-crosslinking a subset of the sonicated material and then running it on an agarose gel. This is what I have been doing to date, however, I think what I have been visualising is mostly RNA not DNA.
So, I have recently tried preparing them the same as I would my INPUT samples (RNase A treated, then Proteinase K treated, Reverse-crosslinked, P:C:Ia cleaned, etc) and run the cleaned products on a gel. After this thorough process I have no DNA product on my gel.
Can anyone suggest a 'standard' procedure that everyone should be following?