Nuclei were isolated for PRO-seq and run-on reactions were performed with biotinylated nucleotides. For ChIP-seq, isolated nuclei were sonicated to shear chromatin and IPed with two different antibodies (CS and MM) and non-specific IgG. Input DNA was also sequenced for each condition. PRO-seq libraries were performed according to the paper: Kwak H, Fuda NJ, Core LJ, Lis JT. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 2013 Feb 22;339(6122):950-3. PMID: 23430654. ChIP-seq libraries were prepared the standard way using Illumnia TRU-seq adpapters.