S04203_iPSC_C5P18_UDID170_ATAC_R07L01S02
Detailed methods are found in doi 2024.04.10.588874. ATAC-seq samples were processed using a modified version of the Buenrostro et al. protocol. Briefly, frozen nuclear pellets were thawed on ice and tagmented in total volume of 25ul in permeabilization buffer containing digitonin (10mM Tris-HCl pH 7.5, 10mM NaCl, 3mM MgCl2, 0.01% digitonin) and 2.5ul of Tn5 from Nextera DNA Library Preparation Kit (Illumina) for 45-75min at 37C in a thermomixer (500 RPM shaking). We included a double size selection step during purification using AMPure XP DNA beads (Beckman Coulter). To eliminate confounding effects due to index hopping, libraries within a pool were indexed with unique pairs of i7 and i5 barcodes. Libraries were amplified for 12 cycles using High-Fidelity 2X PCR Master Mix (NEB) in total volume of 25ul in the presence of 800nM of barcoded primers (400nM each) custom synthesized by Integrated DNA Technologies (IDT) and sequenced with either 100 bp paired-end or 150 bp paired-end reads on an Illumina HiSeq4000 or Illumina NovaSeq 6000.