Protocol update to: Genome-wide interrogation of protein-DNA interactions in mammalian cells using ChIPmentation

Mapping the genomic locations of chromatin-associated proteins, such as transcription factors and histone modifications, is key to understanding the mechanisms of transcriptional regulation. ChIPmentation offers a simple and robust way of investigating the genomic binding sites of a protein using relatively low-input material. Here, we present a detailed protocol for the key steps that lead to a successful ChIPmentation experiment, as well as a quick analysis pipeline to examine the data. For complete details on the use and execution of this protocol, please refer to Schmidl et al. 1 For example data produced by this protocol, please refer to Henriksson et al. 2 and Zhang et al. 3 This protocol is an update to Xu et al. 4 • Preparation of a transposase-assisted ChIP-seq library • A simpler and cheaper approach than traditional ChIP-seq • A sensitive and reliable method for transcription factors and histone modifications • A simpler and faster computational workflow for ChIP-seq data analysis Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Mapping the genomic locations of chromatin-associated proteins, such as transcription factors and histone modifications, is key to understanding the mechanisms of transcriptional regulation. ChIPmentation offers a simple and robust way of investigating the genomic binding sites of a protein using relatively low-input material. Here, we present a detailed protocol for the key steps that lead to a successful ChIPmentation experiment, as well as a quick analysis pipeline to examine the data.