GSM9320973: KPC_MYC_ChIPseq_RBRIII_IP_r1; Mus musculus; ChIP-Seq
To crosslink cells following treatment, 1% v/v formaldehyde was added to the cell culture medium and incubated 5 min rotating at RT. 125 mM glycine were added to stop the reaction and incubated for 5 min rotating at RT. Cells were then harvested in ice-cold PBS containing protease and phosphatase inhibitors (Sigma Aldrich). Cells were centrifuged (1,500 rpm, 20 min, 4°C) and the pellet was resuspended in ChIP lysis buffer I (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40). For spike-normalization, 10% murine NIH3T3 cells were added based on the cell number. After 20 min incubation on ice, nuclei were pelleted by centrifugation (1,500 rpm, 20 min, 4°C) and subsequently lysed by incubation in ChIP lysis buffer II (10 mM Tris pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% NP-40, 1% sodium deoxycholate, 0.1% SDS) for 10 min on ice. The chromatin was fragmented using the Covaris Focused Ultrasonicator M220 (50 min; cycles/burst, 200; peak power, 75; duty factor, 10), and the required fragment size of 150-300 bp was validated by agarose gel electrophoresis. The fragmented chromatin was collected by centrifugation (14,000 rpm, 20 min, 4°C). For each IP, 100 µl of each Protein A and Protein G-coupled Dynabeads (Thermo Fisher Sientific) were pre-incubated overnight with 15 µg antibody in the presence of 5 mg/mL BSA at 4°C. Subsequently, beads were added to the chromatin and incubated overnight at 4°C on a rotating wheel. Immunoprecipitated protein-chromatin complexes were washed 3 times each with ice-cold ChIP wash buffer I (20 mM Tris pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), ChIP wash buffer II (20 mM Tris pH 8.1, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), ChIP wash buffer III (10 mM Tris pH 8.1, 250 mM LiCl, 1 mM EDTA, 1% NP-40, 1% sodium deoxycholate; including a 5 min incubation at 4°C), and once with ice-cold TE buffer. Protein-chromatin complexes were eluted twice by incubating in 150 µl elution buffer 100 mM NaHCO3, 1% SDS) for 15 min at RT. To remove potential RNA contaminations, IP and input samples were treated with RNase A for 1 h at 37°C. Samples were de-crosslinked by incubation at 65°C shaking overnight, and then treated with Proteinase K for 2 h at 45°C to degrade the protein. The amount of DNA was quantified using Quant-iT PicoGreen dsDNA assay (Thermo Fisher Scientific) Libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer's instructions.