Illumina NovaSeq 6000 paired end sequencing; Identification of SOX11 binding sites through CUT&RUN sequencing in the neuroblastoma cell lines IMR-32, CLB-GA, NGP and SH-EP
Identification of SOX11 binding sites through CUT&RUN sequencing in the neuroblastoma cell lines IMR-32, CLB-GA, NGP and SH-EP
0.5M cells were harvested for CUT&RUN. CUT&RUN was performed using Cutana pA/G-MNase (Epicypher, 15-1016) according to the manufacturer's protocol. Cells were grown in RPMI1640 medium supplemented with 10% foetal bovine serum, 2mM L-Glutamine and 100 IU/ml penicillin/streptaviding at 37°C in a 5% CO2 humid atmosphere. SH-EP cells were treated with 0.1ug/ml doxycycline for 48h to induce SOX11 over expression. Retrieved genomic DNA was purified with the MinElute PCR purification kit and eluted in 10 mL of buffer EB. Sequencing libraries were prepared with the automated Swift 2S system.