Illumina HiSeq 4000 paired end sequencing; ATAC-seq of HepG2 cells
ATAC-seq of HepG2 cells
Cells were harvested via trypsinization, followed by a series of wash steps. 100,000 cells of each were spun down at 550xg for 5min, 4C. Supernatant was removed; 50uL of PBS was added to wash pellet. Spin conditions remained the same. The cell pellet was resuspended in 50ul cold lysis buffer (1 mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630), spun down immediately at 550xg for 10min, 4C. The nuclei resuspended in the transposition reaction mix (2x TD Buffer (Illumina Cat #FC-121-1030, Nextera), 2.5ul Tn5 Transposes (Illumina Cat #FC-121-1030, Nextera) and Nuclease Free H2O) on ice. The transposition reaction was incubated at 37C for 45min. The transposed DNA was then purified using a Qiagen MinElute Kit with 10.5ul elution buffer. The transposed library was then PCR amplified using Nextera primers for 12 cycles. The PCR reaction was subsequently cleaned up using AMPureXP beads (Agencourt).
Experimental Factor: replicate
2