GSM4568830: ATACseq of MA1L_vector, 0_IFNG replicate 2; Mus musculus; ATAC-seq
200,000 of vector or sgKmt2d transduced primary liver tumor cells (MA1L) were seeded into 12-well plate, and 0, or 10 ng/ml IFN-γ were added to treated them for 24 h. After treatment, the cell nuclei were collected for ATAC-seq using a protocol as previously described. Briefly, cells from different treatment group were counted and 50,000 cells were collected by centrifuge at 500g for 5 min. After washing once with 50 μl of cold 1× PBS, the cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500 g for 10 min using a refrigerated centrifuge, and the pellet was resuspended in the transposase reaction mix (25 μl 2× TD buffer, 2.5 μl transposase (Illumina) and 22.5 μl nuclease-free water). The transposition reaction was carried out for 30 min at 37°C. After transposition reaction, the sample was purified using a Qiagen MinElute kit, and using 1× NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2 using the following PCR conditions: 72°C for 5 min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. To assure the PCR cycles, the full libraries were amplified for five cycles, and then 5 μl was used for Sybr Green qPCR. After determing the cycle number, the remaining 45 μl were amplified. The libraries were purified using AMPure XP beads.
GEO Accession
GSM4568830