ChIP-sequencing (ChIP-seq) combines chromatin immunoprecipitation (ChIP) with DNA sequencing and has been highly used for studying DNA-protein interactions. Yet, most implementations of ChIP-seq are inefficient and slow requiring two to three days for completion of the complicated and often manual workflow.

To overcome these issues, we combined our validated automated ChIP-seq with the Covaris Adaptive Focused Acoustics (AFA) technology to streamline and significantly reduce the overall workflow time for ChIP-seq. In our study, we tested the ability of AFA to enhance the binding kinetics of antibody-epitope association, improve signal-to-noise ratios, and decrease total processing time. We evaluated a range of epitopes including major histone modifications such as H3K4me3 which is associated with open chromatin and forms narrow peaks, H3K27me3 which is linked to repressed chromatin and binds to wide regions, and H3K27ac associated with open chromatin, and both wide enhancer loci as well as narrow promoter regions.

Additionally, we are also studying the capacity of the AFA to augment the IP step of DNA associated proteins such as CTCF and validated our test conditions using two cell types.

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University of California San Diego