Using the Magna ChIP™ HT96 kit, high-throughput chromatin immunoprecipitation (ChIP) can be performed on up to 96 samples in a single experiment using as few as 10,000 cells per well. The protocol uses a single buffer for sonication, immunoprecipitation, and washing, which can yield good sensitivity and low backgrounds. The Magna ChIP HT96 protocol has been designed for immunoprecipitation and recovery of DNA; in many cases, a separate DNA purification step is not required for downstream analysis.