GSM5593053: ATACseq_MC38_3hours_RG6146_TNF; Mus musculus; ATAC-seq
Sonication was performed using a Covaris ultrasonicator at maximum power for 16 minutes to achieve an average DNA fragment size of 300-500bp. Immunoprecipitation reactions were performed overnight at 4ºC by diluting sonicated chromatin 1:1 in ChIP dilution buffer (20 mM Tris-HCl, 150 mM NaCl2, 2 mM EDTA, 1% Triton-X, and phosphatase/protease inhibitors in water) and addition of a 1:1 ratio of protein A and G magnetic beads (Life Technologies) were used to bind crosslinked protein/DNA. Libraries were generated using the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645) and sequenced on an Illumina NextSeq 550 with 75 b.p. paired-end reads. Library QC and quantification was performed using D1000 high-sensitivity screen tape with 4200 TapeStation Instrument (Agilent Technologies) and size selected for between 200 bp and 500 bp using a Pippin Prep system (Sage Science).