title: ATAC-seq of human: adult female bone_marrow tumor: Sample H_KA-345701-atac1
design: Transposase-mediated chromatin accessibility profiling of primary AML cells was performed using the Nextera library preparation kit as described in (Buenrostro et al., 2013) using 75,000150,000 viable cells per sample. Briefly, cells were pelleted, washed once in 50 uL cold 1× PBS, and then resuspended in 50 uL cold ATAC lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630). Lysed cells were then immediately centrifuged at 500 × g for 10 min at 4°C, and cell nuclei were resuspended in 25 uL Nextera tagmentation buffer (Illumina) for transposition with 2.5 uL of Nextera transposase enzyme (Illumina) in a total volume of 50 uL at 37°C for 30 minutes. DNA was purified with Qiagen MinElute columns before amplification with sample-specific primers for a total 912 cycles (the exact cycle number was determined via qPCR analysis after 5 cycles). Libraries were either size-fractionated into small (<300 bp) and large (300800 bp) libraries, or a single library (100500 bp)
attributes.tag: alignment_software
attributes.value: BWA_MEM