Illumina HiSeq 2000 paired end sequencing; Epichromatin HL-60/S4
Epichromatin HL-60/S4
HL-60/S4 cells were cultured in RPMI-1640 medium with 10% heat-inactivated fetal calf serum and 1% penicillin/streptomycin. Cells were differentiated into granulocytes by addition of all-trans ratinoic acid and into macrophage by phorbol ester. Cells were fixed, lysed and incubated with primary antibody, either PL2-6 or 1H6, before they were fixed again and sonicated in Covaris micro-chambers. The harvested supernatant was incubated with Protein A/G agarose to bind the epichromatin-antibody complex, and the remainder (input) represents the total nuclear chromatin. The epichromatin (IP) was eluted from the complex. DNA was purified with QIAquick PCR Purification Kit (QIAGEN). ChIP-seq libraries were prepared with NEB Next Chip Seq DNA Sample Prep Kit according to the manufacturers protocol.