Can I use the Zymo kit for DNA purification after the immunoprecipitation?
As the DNA purification step is critical and the loss of precious DNA might occur at this step, we recommend our optimized protocol from the MeDIP kit. Recently we have compared different DNA purification methods of immunoprecipitated DNA. We can conclude that Phenol/chloroform & ETOH precipitation dramatically improved our yield (93%) of methylated product (qPCR data) compared to the use of Zymo (43%) and Qiagen (52%) columns.