Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a widely used assay to uncover the function of proteins of interest by generating a snapshot of the protein’s binding sites in an organism at a certain stage given specific conditions. Previous publications provide recommendations for ChIP-Seq analysis, but the guidelines are curated for human, mouse, fly, and worm genomes. More specifically, lists of regions of artificial signal for removal, called “blacklists”, were generated for only the four selected organisms, and therefore downstream analyses in other species are vulnerable to the unmasked noise. Methods to more easily identify ChIP-seq artifacts and then perform ChIP-Seq analysis is introduced and discussed in Chapter 1. In Chapters 2-4, we applied this pipeline to ChIP-Seq experiments in Arabidopsis, the plant model organism, as supportive evidence to understanding the role of specific proteins during floral development. In Chapter 2 analysis of gene expression and chromatin compaction with transcription factor LFY ChIP-seq annotation reveals the role of LFY-binding as a prerequisite for unlocking genes necessary for inflorescence. In Chapter 3, ChIP-Seq was used to reveal where bZIP transcription factor FD recruits TFL1 to compete for regulation of cell fate within the primordia of inflorescence. In Chapter 4, comparisons of ChIP-Seq experiments from different publications highlight recent advances to the collective understanding of floral reproductive development. Plants provide interesting models for studying cell fate since they are continuously generating and developing new organs for either growth or reproductive development. In this dissertation a ChIP-Seq pipeline was manufactured and applied to further the collective effort in understanding these activities.