Exploring the Genomic Landscape: An In‐depth ChIP‐seq Analysis Protocol for Uncovering Protein‐DNA Interactions

Abstract Chromatin immunoprecipitation followed by sequencing (ChIP‐seq) is a widely employed technique for investigating protein‐DNA interactions. However, the absence of a standardized and clear workflow necessitates researchers to independently assemble methodologies from diverse resources. This lack of uniformity hampers reproducibility and makes version control a complex endeavor, thereby limiting the accessibility of ChIP‐seq analyses to individuals with extensive training in bioinformatics. In light of these challenges, we have developed an executable protocol that addresses these limitations. Our protocol encompasses all aspects of ChIP‐seq analysis, ranging from quality control of raw reads to peak calling and downstream functional analyses. We have implemented two distinct approaches for peak calling, providing researchers with flexibility to choose the most suitable method for their specific experimental needs. This protocol will contribute to the scientific community by providing a standardized and clear resource that will enhance the reproducibility and accessibility of ChIP‐seq analyses. © 2023 Wiley Periodicals LLC. Basic Protocol : ChIP‐seq analysis workflow Alternative Protocol : Call differentially enriched peaks by using MACS3