NextSeq 500 sequencing; ATAC-seq in IMR-32, CLB-GA and SH-EP neuroblastoma cell lines.
ATAC-seq in IMR-32, CLB-GA and SH-EP neuroblastoma cell lines.
50,000 cells were harvested and spin down for 5 min at 800g. Cells were grown in RPMI1640 medium supplemented with 10% foetal bovine serum, 2 mM L-Glutamine and 100 IU/ml penicillin/streptavidin at 37Â°C in a 5% CO2 humid atmosphere, supplemented with 10% tetracyclin-free FBS to avoid leakage. ATAC-seq was performed as previously described with minor changes (Buenrostro et al. 2015). 50,000 cells were lysed and fragmented using digitonin and Tn5 transposase (Nextera DNA Library Prep Kit, cat#FC-121-1030)). Samples were purified using the DNA clean & concentrator kit from Zymo (cat#D4013). The transposased DNA fragments were amplified using the KAPA HiFi HotStart Readymix (cat#07 958 927 001) and purified using Agencourt AMPure XP beads (Beckmamn Coulter, cat#A63881). Library concentrations were measured with the Illumina Kapa Library quantification kit (Lightcycler 480 qPCR mix cat#KK4854)