H3K27Ac ChIP-seq in LNCaP Cells

H3K27Ac ChIP in LNCaP cells was performed as previously described^{45 (link)}. Briefly, ten million cells were fixed using 1% formaldehyde (Thermo Fisher Scientific) for 10 min at room temperature. Chromatin was sheared in ice-cold lysis buffer (50 mM Tris, 10 mM EDTA, 1% SDS with protease inhibitor) to 300–500 base pairs using the Covaris E210 sonicator. The sample was incubated with 1 μg H3K27Ac antibody (Diagenode, C15410196, Denville, NJ) coupled with protein A and protein G beads (Life Technologies, Carlsbad, CA) at 4 °C overnight. The chromatin was washed with RIPA washing buffer (0.05 M HEPES pH 7.6, 1 mM EDTA, 0.7% Na Deoxycholate, 1% NP-40, 0.5 M LiCl). After decrosslinking, IP DNA as well as its input were extracted using QIAGEN Qiaquick columns, and sequencing libraries prepared using the ThruPLEX-FD Prep Kit (Rubicon Genomics, Ann Arbor, MI). Libraries were sequenced using 75-base pair single reads on Illumina platform at DFCI-MBCF.