ChIP assays were performed as previously described with minor modifications (O'Geen et al. 2010). 50 μg of sonicated chromatin was incubated with 3 μg of monoclonal anti-Flag antibody (SIGMA M2 F1804). After incubation with 3 μg of rabbit anti mouse serum, StaphA cells (Sigma-Aldrich) were used to collect the immunoprecipitates. After washes and reversal of DNA-RNA-protein cross-links The entire ChIP sample was used to create an Illumina sequencing library using the KAPA library preparation kit (KAPA Biosystems) and NEXTflex DNA barcodes (BIOO Scientific).