GSM8529411: 3782-BW-25 ATAC-seq; Homo sapiens; ATAC-seq
Human liver wedge biopsies were supplied by the Penn Transplant Institute. Samples were derived from human livers deemed fit for transplantation, and were collected at the time of the surgery. Samples were flash frozen and stored at -80 C. Chromatin accessibility profiles were generated using a modified Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) called Omni-ATAC. Briefly, approximately 20 mg of tissue was dounce homogenized in a homogenization buffer. Tissue homogenate was layered over Iodixanol density gradient and spun. Nuclei were extracted post-centrifugation and quantified using a hemocytometer. Approximately 50,000 nuclei were rinsed and added to the Omni-ATAC reaction mix. Transposition reactions were incubated at 37 C for thirty minutes. Reactions were cleaned with spin columns and eluted. Polymerase chain reaction (PCR) was initially performed for five cycles. At this point, a qPCR reaction was performed to determine the additional number of PCR cycles to use. The additional number of PCR cycles is determined by calculating the qPCR cycle at which the fluorescence intensity is equal to one-third the maximum fluorescent intensity of the reaction. Libraries were purified and profiles were measured using Bioanalyzer High-Sensitivity DNA Analysis Kit (Agilent). Libraries that pass visual quality control and concentration checks were frozen at -20 C.