An integrated microfluidic chromatin immunoprecipitation assay dramatically improves the collection efficiency of ChIP DNA from cells. Immunoprecipitation of chromatin fragments is conducted in a microfluidic chamber with a large fraction of its volume (e.g., ˜15-40%) occupied by magnetic immunoprecipitation (IP) beads. Oscillating washing of the beads, enabled by, e.g., solenoid valves (controlled by a computer) and high pressure attached to both ends of the microfluidic chamber, effectively removes unbound chromatin and produces high-quality ChIP DNA. ChIP DNA produced by an example device generates excellent results in the subsequent DNA library preparation. The ChIP-seq (i.e., ChIP followed by next-generation sequencing) results match very well with public data generated using much larger cell sample sizes and a conventional approach.