ATAC-Seq Data for HG01952 Replicate 2
For ATAC-seq library preparation, cells from each LCL were harvested upon reaching confluence, with cell numbers ranging from approximately 100,000 to 200,000. The cells were centrifuged at 500 g for 10 minutes at 4C. Following centrifugation, the supernatant was carefully aspirated, and the cell pellets were resuspended and lysed in 100 l of ATAC-seq RSB (10 mM Tris, pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin. This mixture was pipetted up and down before incubation on ice for 3 minutes, facilitating cell membrane disruption while preserving nuclear integrity. Subsequently, 1 mL of ATAC-seq RSB with 0.1% Tween-20 was added to the lysate, mixed gently, and nuclei were pelleted by centrifugation at 1000 g for 10 minutes at 4C. The supernatant was discarded, and nuclear pellets were carefully resuspended in 25 l of 2x TD buffer (20 mM Tris-HCl, pH 7.6, 10 mM MgCl2, 20% Dimethyl Formamide). The quality and quantity of isolated nuclei were assessed using trypan blue exclusion under a microscope. For the transposition reaction, 25 l of transposition mix (2.5 l of Tn5 Transposase, 16.5 l of PBS, 0.5 l of 1% digitonin, 0.5 l of 10% Tween-20, and 5 l of nuclease-free water) was added to the nuclei. This mixture was incubated at 37C for 30 minutes, with gentle tapping every 10 minutes to ensure mixing. The reaction was purified using Zymo DNA Clean and Concentrator-5 columns according to the manufacturer's instructions. Library amplification was performed by adding Nextera primers to the transposed DNA and cycling the reaction for 9 cycles. Post-amplification, libraries were cleaned using Sera-Mag Select beads with a double size selection protocol to ensure the removal of unwanted fragments. Final ATAC-seq libraries were quantified using Qubit fluorometric quantitation. Sequencing of the paired-end libraries was conducted on an Illumina NextSeq 500 platform.