UC San Diego

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a technique widely used for systematic in vivo mapping of protein-DNA binding and interaction. However, the experimental process of manual ChIP-seq is laborious and time-consuming. Therefore, to improve efficiency and accelerate the workflow, the goal of my project is to develop an automated ChIP-seq protocol with a robotic liquid handling platform and use it to systematically evaluate the ChIP-seq assay conditions. In the experimental results, we have demonstrated that our automated high-throughput ChIP-seq workflow was reproducible and maintained similar signal-to-noise ratio as the manual workflow, while reducing human errors and total experimental time. The automated ChIP-seq has useful applications, such as antibody titration and evaluation of multiple conditions at once. Besides automation, we assessed crosslinking conditions, comparing formaldehyde (FA) single crosslinking and DSG/FA double crosslinking for the ChIP-seq of chromatin regulator SETD5. We also optimized chromatin shearing conditions in the ChIP-seq workflow, as we tested different sonicators as well as evaluated multiple different lysis buffers for shearing.