GSM8917928: dRBSdATG, xylA, UTR 300bp, BCM-treated, replicate 1; Escherichia coli str. K-12 substr. MG1655; ChIP-Seq
E. coli cells induced for 4 hours with proper inducer were cross-linked by 1% formaldehyde at room temperature for 30 min. The cross-linked cells were harvested and lysed, followed by sonication for DNA fragmentation. If necessary, cells were treated with 50 μg/mL bicyclomycin (BCM) for 30 minutes or 150 μg/mL rifampicin for 15 minutes prior to harvest. The sheared DNA was immunoprecipitated by proper antibodies (anti-RNAP β or c-Myc). After binding to chromatin beads, immunoprecipitated DNA was end-repaired, dA-tailed, and ligated with the first adapter using the KAPA HyperPrep Kit (KAPA Biosystems). Adapter-ligated DNA samples were then nick-repaired and exonuclease-treated. The DNA samples were eluted from the beads by reversing protein-DNA crosslinking at 65 °C. Primer extension and second adapter ligation were performed in sequence. Finally, the DNA samples were enriched by PCR, using KAPA HotStart ReadMix in HyperPrep Kit (KAPA Biosystems). DNAs after each reaction were purified and size-selected using either AMPure XP beads (Beckman Coulter, Brea, CA, USA) or Zymo DNA Clean & Concentrator (Zymo, Irvine, CA, USA).