GSM7653931: K562; Homo sapiens; OTHER
After immune cell, target cells and (NF-kB) conjugated beads were co-encapsulated and incubated for 6 hours- time needed to observe sufficient killing of K562 by NK92 cells- the antibody coated beads, capturing the transcription factor interacting with the DNA from the dead target cell (Transcription factor + DNA complex), were pulled out from the droplets using a magnetic rack (0.5-0.7 mL tube Magnetic Rack, Amazon) for 10 minutes. The beads were washed with 0.1M MES buffer pH 5.2 (Coupling Buffer) and a simple DNA isolation protocol was performed using a DNA Clean & ConcentratorTM-5 (Cat# D4014, Zymo Research Corporation). After the DNA samples quality control: (1) The DNA fragments are repaired, dA-tailed. (2) The DNA fragments with A tail are ligated to sequencing adaptors. (3) The final DNA library is obtained by size selection and PCR amplification. ChIP DNA has two kinds of lib our internal kit, provided with enough DNA amount. The other is low input, which applies kit preparation workflow. One is based on regular input and applies our internal kit, provided with enough DNA amount. The other is low input, which applies kit called NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®. Both workflows of library construction are as following graph.