GSM9396710: TRF2 ChIP-nexus Control rep1; Drosophila melanogaster; ChIP-Seq
10e7 Kc167 cells were fixed with 1% formaldehyde in culture media at room temperature for 10 min with rotation. Fixed cells were washed with cold PBS, incubated with Orlando and Paro's Buffer (0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 10 mM Tris-HCl pH 8.0, with freshly added Protease Inhibitor) for 10 min at room temperature with rotation, and then centrifuged and re-suspended in ChIP Buffer (10 mM Tris-HCl, pH 8.0; 140 mM NaCl; 0.1% SDS; 0.1% sodium deoxycholate; 0.5% sarkosyl; 1% Triton X-100, with freshly added Protease Inhibitor). Sonication was performed with a Bioruptor Pico for five rounds of 30 s on and 30 s off. Chromatin extracts were then centrifuged at 16,000 g for 5 min at 4° C. Supernatants were used for ChIP. NOTE: This sample was prepared following a previous version of the ChIP-nexus protocol. Chromatin extracts were added to the antibody-bound beads (10 ug antibody per 50 ul Dynabeads Protein A + 50 ul Dynabeads Protein G) and incubated at 4°C overnight with rotation and then washed with Nexus washing buffer A to D (wash buffer A: 10 mM Tris-EDTA, 0.1% Triton X-100, wash buffer B: 150 mM NaCl, 20 mM Tris-HCl, pH 8.0, 5 mM EDTA, 5.2% sucrose, 1.0% Triton X-100, 0.2% SDS, wash buffer C: 250 mM NaCl, 5 mM Tris-HCl, pH 8.0, 25 mM HEPES, 0.5% Triton X-100, 0.05% sodium deoxycholate, 0.5 mM EDTA, wash buffer D: 250 mM LiCl, 0.5% IGEPAL CA-630, 10 mM Tris-HCl, pH 8.0, 0.5% sodium deoxycholate, 10 mM EDTA). End repair and dA-tailing were performed using the NEBNext End Repair Module and the NEBNext dA-Tailing Module. ChIP-nexus adaptors with mixed fixed barcodes (CTGA, TGAC, GACT, ACTG) were ligated with Quick T4 DNA ligase and converted to blunt ends with Klenow fragment and T4 DNA polymerase. The samples were treated with lambda exonuclease and RecJf exonuclease. After each enzymatic reaction, the chromatin was washed with the Nexus washing buffers A to D and Tris buffer (10 mM Tris, pH 7.5, 8.0, or 9.5, depending on the next enzymatic step). The chromatin was then eluted and subjected to reverse crosslinking and ethanol precipitation. Purified single-stranded DNA was then circularized with CircLigase, annealed with oligonucleotides complementary to the BamHI restriction site and linearized by BamHI digestion. The linearized single-stranded DNA was purified by ethanol precipitation and subjected to PCR amplification with NEBNext High-Fidelity 2X PCR Master Mix and ChIP-nexus primers.