title: ATACseq of 92-1 human uveal melanoma cell line treated with 100nM BRM011
design: 100,000 cells were processed for ATACseq using OMNI-ATACseq protocol (38). After tagmentation, samples were purified using Zymo DNA clean and concentration kit according to manufacturers protocol. Purified DNA was used for library amplification using Nextera Index kit (Illumina) and NEBNext High-Fidelity PCR master mix (New England biolabs). Number of amplification cycles was determined individually for each sample by qPCR using SYBR green and calculated as number of PCR amplification cycles required to one-third maximum fluorescent intensity. All libraries were amplified with <11 cycles to ensure sufficient library complexity. After amplification, libraries were purified using AMPure XP beads. Final product quality and concentration was determined using the D5000 DNA Tape on the Agilent Tapestation. The samples were diluted to 8 nM in Qiagen Elution Buffer (Qiagen material # 1014609), denatured, and loaded at about 6.4 picomolar on a Miseq at 75 base pair paired end with 8 base pair dual indexes using the MiSeq Reagent Kit v3, 150 cycles (Cat# 15043893). Resulting sequence data was used to recalculate sample concentration adjusting for sample representation. Using these updated concentrations, samples were again diluted to 8 nM in Qiagen Elution Buffer (Qiagen material # 1014609), denatured, and loaded at 6.4 picomolar on an Illumina cBOT using the HiSeq 4000 PE Cluster Kit (Cat# PE-410-1001). The ATAC-Seq libraries were sequenced on a HiSeq 4000 at 75 base pair paired end with 8 base pair dual indexes using the HiSeq 4000 SBS Kit, 150 cycles (Cat# FC-410-1002). The sequence intensity files were generated on instrument using the Illumina Real Time Analysis software.
library_name: 92.1_BRM011-100nM_R2_ATAC