iPSC-RPE ATAC: Sample 5980b386-00fa-41c0-9e57-7c8c15b25d65
We performed ATAC-seq using the protocol from Buenrostro et al. (Buenrostro et al., 2013) with small modifications. Frozen nuclear pellets of 5 x 104 cells each were thawed on ice and tagmented in permeabilization buffer containing digitonin. Tagmentation was carried in 25µl using 2.5µl of Tn5 from Nextera DNA Library Preparation Kit (Illumina) for 60 min 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 for iPSC-RPE were amplified for 12 cycles. Libraries were sequenced to approximately 80M 150bp paired end reads on the HiSeq 4000 (Illumina) platform. 
alignment_software
STAR