Murine_Trachea_p63_ChIP_R2
Murine tracheas were surgically removed and the luminal epithelium was         exposed to formaldehyde (1%) within 60 seconds of sacrifice (immediateex vivo processing).         After cross-linking, the tracheas were scraped in PBS with protease inhibitors         (cOmplete-Mini-Roche) to remove the epithelial cell layer. Each ChIP replicate experiment         was from 50 tracheas, which yielded approximately 50 million cells. After sonication and         immunoprecipitation of cell lysates with antibodies specific to p63 (H129; Santa Cruz), p73         (EP436Y; Abcam), and Pol II (sc-899; Santa Cruz) cross-linked DNA was isolated and sonicated         using a Bioruptor to approximately 300 bp in length. Libraries for each ChIP were prepared         by ligating Illumina adapter sequences to the sheared DNA fragments and sequencing at the         Vanderbilt Technologies for Advanced Genomics core. All three ChIP-seq experiments were         conducted in duplicate. Input DNA was harvested from the pooled, cross-linked, and sonicated         trachea samples which did not undergo immunoprecipitation, as a comparison control for         systematic bias.