iPSC ATAC-seq: Sample 22cf7287-5132-4a61-9cf7-04fff392e2c2
We performed ATAC-seq on 152 iPSC samples using the protocol from Buenrostro et al. (Buenrostro et al., 2013) with small modifications. Frozen nuclear pellets of 2.5 x 104 PSCs were thawed on ice and tagmented in total volume of 25µl in permeabilization buffer containing digitonin and 2.5µl of Tn5 from Nextera DNA Library Preparation Kit (Illumina) for 45-75min at 37°C in a thermomixer (500 RPM shaking). To eliminate confounding effects due to index hopping, all libraries within a pool were indexed with unique i7 and i5 barcodes. Libraries were amplified for 12 cycles using NEBNext® High-Fidelity 2X PCR Master Mix (NEB) in total volume of 25µl in the presence of 800nM of barcoded primers (400nM each) from custom synthesized by Integrated DNA Technologies (IDT). Each library was independently sequenced twice on Illumina HiSeq 4000 with paired-end 150bp reads.
alignment_software
STAR