Other ; This is the author accepted manuscript. It is under an indefinite embargo pending publication by Bio-protocol. ; Abstract ; DNA immunoprecipitation followed by deep sequencing (DIP-Seq) is a key tool in identifying and studying the genome-wide distribution of N-6-methyl-deoxyadenosine (dA$^{6m}$). This protocol describes the method to perform dA$^{6m}$ DNA immunoprecipitation (DIP), as was applied to characterize the first dA$^{6m}$ methylome analysis in higher eukaryotes (Koziol $\small \textit{et al}$, 2015). ; Other ; Long-Term Human Frontiers Fellowship (LT000149/2010-L), Medical Research Council (Grant ID: G1001690), Isaac Newton Trust Fellowship (Grant ID: RG76588), Biotechnology and Biological Sciences Research Council (Grant ID: BB/M022994/1), Wellcome Trust (Grant ID: 101050/Z/13/Z), Wellcome Trust Core Grant (Grant ID: 092096/Z/10/Z), Cancer Research UK (Grant ID: C6946/A14492)