ATAC-Seq of homo sapiens: pancreatic islets
We generated ATAC-seq data from four of the human islet samples with a protocol as previously described12. For Islet samples ISL_3 and ISL_4, permeabilized nuclei were obtained by resuspending cells in 250L Nuclear Permeabilization Buffer [0.2% IGEPAL-CA630 (I8896, Sigma), 1mM DTT (D9779, Sigma), Protease inhibitor (05056489001, Roche), 5% BSA (A7906, Sigma) in PBS (10010-23, Thermo Fisher Scientific)], and incubating for 10 min on a rotator at 4C. Nuclei were then pelleted by centrifugation for 5 min at 500 xg at 4C. The pellet was resuspended in 25L ice-cold Tagmentation Buffer [33 mM Tris-acetate (pH = 7.8) (BP-152, Thermo Fisher Scientific), 66 mM K-acetate (P5708, Sigma), 11 mM Mg-acetate (M2545, Sigma), 16 % DMF (DX1730, EMD Millipore) in Molecular biology water (46000-CM, Corning)]. An aliquot was then taken and counted by hemocytometer to determine nuclei concentration. Approximately 50,000 nuclei were resuspended in 20L ice-cold Tagmentation Buffer, and incubated with 1L Tagmentation enzyme (FC-121-1030; Illumina) at 37C for 30min with shaking 500 rpm. The tagmentated DNA was purified using MinElute PCR purification kit (28004, Qiagen). The libraries were amplified using NEBNext High-Fidelity 2X PCR Master Mix (M0541, NEB) with primer extension at 72C for 5 min, denaturation at 98C for 30s, followed by 8 cycles of denaturation at 98C for 10 s, annealing at 63C for 30 s and extension at 72C for 60 s. Amplified libraries were then purified using MinElute PCR purification kit (28004, Qiagen), and two size selection steps were performed using SPRIselect bead (B23317, Beckman Coulter) at 0.55X and 1.5X bead-to-sample volume rations, respectively. Each library was then sequenced on an Illumina NextSeq500 or HiSeq4000 to a depth of >= 25 million usable reads pairs (i.e. after mapping, filtering, and elimination of PCR duplicates as described in the data processing section).