Detect accessible chromatin using ATAC sequencing in the Kasumi-1 cell line transfected with PHF19 shRNA or scrambled control shRNA
To investigate the function of PHF19 in the regulation of chromatin accessibility in t(8;21) AML, we established Kasumi-1 cell line in which PHF19 gene has been knocked down by shRNA. We then performed chromatin accessibility analysis using data obtained from ATAC-seq of the PHF19 knockdown cells and the scrambled control cells. Overall design: Stable silencing of the PHF19 gene in Kasumi-1 cells was achieved through a lentiviral vector-based system for RNAi (GV493/hU6-MCS-CBh-gcGFP-IRES-puromycin) constructed by GeneChem Technologies (China). Transfection of lentivirus was conducted according to the manufacturer's instruction. Kasumi-1 cells were seeded into 6-well plates overnight before transfection and the medium was changed approximately 12 to 16 hours after transfection. Forty-eight hours after shRNA transfection, cells were selected with puromycin (2 microgram per milliliter) for at least 24 hours before further investigations.