ATAC-Seq Analysis of 786-M1A Cells

786-M1A cells were treated with 0.6μg/ml doxycycline for 6 days before harvesting at 70% confluency. On the day of harvest, cells were trypsinized, counted, nuclei extracted, and 50,000 cells were used for the ATAC-seq protocol.⁶⁵ (link) ATAC libraries were generated with the Illumina Nextera DNA library preparation kit (FC-121-1030) and purified for amplification with the minElute PCR purification kit (Qiagen 28004). The libraries were amplified for a total of 8-12 cycles using custom Nextera PCR primers and NEBNext PCR master mix (NEB M0541S). The amplified libraries were purified using Agencourt AMPureXP reagents (A63880), profiled on the Agilent 4200 TapeStation System using the high sensitivity D5000 reagents (5067- 5589), pooled in equimolar concentrations, and submitted for sequencing on the Illumina HiSeq4000 platform (SE50).