DAP-seq analysis of HY5 in Arabidopsis thaliana with an optimized protocol

DNA Affinity purification sequencing (DAP-seq) is an in vitro method used to analyze the relative binding affinity of transcription factors to DNA. In this study, we optimized the protocol to homogenize library sizes and improve the reproducibility. We expanded the downstream bioinformatic analysis to assess replicate the robustness by comparing three different measures of peak height, relative binding affinity and control characteristics. To demonstrate these improvements, we generated data for the transcription factor HY5 and the HaloTag control in two replicates.