title: GSM8417727: UVA031  Coronary artery bulk ATAC; Homo sapiens; ATAC-seq
library_construction_protocol: Frozen coronary artery segments were broken down into small pieces using mortar and pestle under dry ice and liquid nitrogen. Nuclei were isolated using iodixanol/sucrose gradients following the Omni-ATAC protocol (Corces et al. Nature Methods 2017). 50,000 nuclei were washed in cold ATAC Resuspension Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) + 0.1% Tween-20 and centrifuged for 10 minutes at 500 g at 4°C. 50,000 nuclei were then resuspended in 50 µl of transposition mix (25 µl 2X TD buffer, 2.5 µl of Tn5 transposase (Illumina), 16.5 µl PBS, 0.01% digitonon, 0.1% Tween-20). Samples were subsequently transposed for 30 minutes at 37°C with shaking (1000 rpm). 50,000 nuclei per sample were used for Tn5 transposition reactions, incubated for 30 minutes at 37C. Transposed DNA was purified using the Zymo DNA Clean and Concentrator-5 Kit and bulk ATAC-seq libraries were generated by PCR amplification and uniquely indexed barcodes. Bulk ATAC-seq libraries were sequenced on an Illumina NovaSeq 6000. Transposed DNA was first purified using the Zymo DNA Clean and Concentrator-5 Kit. Libraries were subsequently constructed and amplified according to Supplementary Protocol 1 in the Omni-ATAC protocol (Corces et al. Nature Methods 2017). Each library underwent 5 cycles of pre-amplification and then additional amplification cycles (determined by qPCR of pre-amplified mixtures)