Purification of nanogram-range immunoprecipitated DNA in ChIP-seq application

As a part of the procedure, immnoprecipitated DNA must undergo purification and library preparation for subsequent high-throughput sequencing. Current ChIP protocols typically yield nanogram quantities of immunoprecipitated DNA mainly depending on the target of interest and starting chromatin input amount. However, little information exists on the performance of reagents used for the purification of such minute amounts of immunoprecipitated DNA in ChIP elution buffer and their effects on ChIP-seq data. Here, we compared DNA recovery, library preparation efficiency, and ChIP-seq results obtained with several commercial DNA purification kits applied to 1 ng ChIP DNA and also investigated the impact of conditions under which ChIP DNA is stored. Overall design: We compared DNA recovery of ten commercial DNA purification reagents from 1 to 50 ng of immunopreciptated DNA in ChIP elution buffer. The immunoprecipitated DNA equivalent to 1 ng of purified DNA was subject to DNA purification and library preparation to evaluate the performance of four better performing purification reagents in ChIP-seq applications.