Schematic of automatic high throughput ChIP-seq protocol and representative data. (A) Primary tissues were isolated and treated with formaldehyde to crosslink protein-DNA contacts. Sonicated lysate was then transferred to an Agilent workstation where it was added to prepared antibody-bound magnetic beads. Wash steps and purification took place on the Agilent workstation. Illumina library preparation took place on separate automated liquid handling system (Beckman) with subsequent HiSeq2000 sequencing. (B) Representation from the UCSC genome browser: a 10 kb region surrounding the Ets2 gene on mouse chromosome 16. DNA binding regions for three factors are shown: CEBPA, RAD21 and H3K4me3. Tracks with a blue background highlight data acquired from our own previously published manual ChIP-seq experiments. Tracks with green background highlight AHT-ChIP-seq data. The height of each track (y-axis) corresponds with uncorrected read depth. Beneath the enrichment track is the RefSeq genome annotation.