title: ChIP-seq of Fairchild mandarin
design: To make antibody-coated beads, 25l Dynabeads Protein A (Thermo Fisher Scientific, 10002D) was washed with ChIP dilution buffer and then incubated with around 1.5g antibodies.The sonicated chromatin samples were centrifuged at 12,000g for 5min and the supernatants were diluted tenfold in ChIP dilution buffer to reduce the SDS concentration to 0.1%. ChIP input aliquots were collected from the supernatants. For all of the samples and replicates, 300500l of diluted chromatin was incubated with the antibody-coated beads at 4C for at least 4h or overnight, then washed, reverse-crosslinked and treated with proteinase K. DNA was purified using a standard phenolchloroform extraction method, followed by ethanol precipitation. The DNA samples were end-repaired using the End-It DNA End-Repair Kit (Epicentre) following the manufacturers protocol. DNA was cleaned up on AMPure beads (Beckman Coulter) with size selection of 100bp and larger.