The dynamic modification of DNA and histones plays a key role in transcriptional regulation through altering the packaging of DNA and modifying the nucleosome surface. These chromatin states, also referred to as the epigenome, are distinctive for different tissues, developmental stages, and disease states and can also be altered by environmental influences. New technologies allow the genome-wide visualization of the information encoded in the epigenome. For example, the chromatin immunoprecipitation (ChIP) assay allows investigators to characterize DNA–protein interactions in vivo. ChIP followed by high-throughput sequencing (ChIP-seq) is a powerful tool to identify genome-wide profiles of transcription factors, histone modifications, DNA methylation, and nucleosome positioning. The low yield of ChIP assays presents a challenge for reproducible and high quality library preparation for high throughput sequencing. Using the automated library preparation system from IntegenX, we prepared ChIP-seq libraries from as little as 1 ng ChIP DNA material. Sequencing of biological replicates on the Illumina platform confirmed a 95%-98% overlap of identified binding sites. Progress of ChIP experiments using limited tissue amounts from rice seedlings as well as other applications of the library automation system will be discussed.