Protocol for transcriptomic and epigenomic analysis of JAK inhibitor sensitivity in IFN-γ-primed human macrophages using ATAC-seq and RNA-seq

Here, we present a protocol for integrating transcriptomic and epigenomic data to analyze Janus kinase (JAK) inhibitor sensitivity in interferon (IFN)-γ-primed human macrophages using assay for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq). We describe steps for ATAC-seq data generation, differential accessibility analysis, and transcription factor motif enrichment. We then detail procedures for integration with RNA-seq data. This systematic approach identifies epigenomic regulatory mechanisms underlying differential JAK inhibitor sensitivity. For complete details on the use and execution of this protocol, please refer to Kwon et al.¹.