GSM2759988: GM12878_rep2; Homo sapiens; ATAC-seq
50,000 cells from two biological replicates of GM12878 were harvested during the exponential growth phase. The cells were spun at 500 g for 5 minutes at 4˚C and then washed using 50 μL of cold 1X PBS.  Samples were then centrifuged at 500 g for 5 minutes.  Cells were lysed in cold lysis buffer (10 mM Tris-HCL, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) and immediately spun at 500 g for 5 minutes at 4˚C. The pellet was then resuspended in the transposase reaction mix (25 μL 2x TD buffer, 2.5 μL transposase and 22.5 μL nuclease-free water; Illumina Nextera).  Following a 30-minute incubation at 37˚C, the samples were purified using the Zymo DNA Clean and Concentrator purification kit. Following the purification, the libraries were amplified with the following PCR conditions: 72°C for 5 minutes; 98°C for 30 seconds; and a total of 10 cycles of 98°C for 10 seconds; 63°C for 30 seconds; 1 minute for 72°C.  Subsequently, the libraries were purified using Agencourt AMpure XP beads; large fragments were filtered by using 0.6x (of PCR mixture volume) magnetic bead volume and taking the supernatant. Primer-dimer and short fragments were removed by collecting bead-associated DNA in a 1:1 (bead solution volume:mixture volume) mix.
GEO Accession
GSM2759988