For ChIP-exo, lysates were clarified from sonicated nuclei and Protein(TFIIB, PolII)-DNA complexes were isolated with IgG antibody. PIP-Seq libraries were prepared for sequencing using standard Illumina protocols; Reference paper: http://www.ncbi.nlm.nih.gov/pubmed/23746353 ChIP-exo libraries were prepared for sequencing using standard Illumina protocols; Reference paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/