ChIP: bright 300bp band after RNAse A - (Nov/09/2007 )
I am trying to work out the DNA sonication for a ChIP assay in Xenopus embryos. After sonication, I treat the samples with RNAse A for 30 minutes and proteinase K for 2 hrs according to the upstate protocol and then load the sample on a 1.4% gel. I consistently see a bright 300 bp band. If I don't treat with RNAse, I get a smear along the entire lane.
To test sonication efficiency, I just reverse the crosslink and follow with phenol/chloroform DNA extraction, then ehtanol precipitation. Worked for me. I believe the Rnase A and Proteinase treatment is only necessary for your IPed samples.