title: GSM8217453: ATAC-seq_Day3_RAS_siTPR_Rep2; Homo sapiens; ATAC-seq
library_construction_protocol: We used the Omni-ATAC protocol (Corces et al., 2017, PMID: 28846090) with some modifications. Briefly, IMR90 cells were harvested by trypsinization and washed with cold PBS. One million cells were resuspended in ice cold ATAC resuspension buffer (ATAC-RSB; 20 mM Tris HCl pH 7.6, 10 mM MgCl2, 20% dimethyl formamide) and 40 strokes in a 1 ml Dounce using a rounded pestle were applied. Debris was pre-cleared by spinning at 100 g for 3 mins. The supernatant was collected and spun again at 1000 g for 5 min to collect the nuclear pellet. The pellet was resuspended in 1 ml ATAC-RSB buffer with 0.1% Tween-20 and spun at 1000 g for 5 min. The nuclear pellet was resuspended in 100 μl TD buffer (10 mM Tris HCl pH 7.6, 5 mM MgCl2, 10% dimethyl formamide) and the Omni-ATAC protocol performed on 50000 nuclei. ATAC-seq libraries were made using adaptor sequences as described previously (Buenrostro et al., 2013, PMID: 24097267). Libraries were assessed for quality and fragment size using the Agilent Bioanalyzer.