GSM8832212: iPSC-CM IndD_DNR_3hr_ATAC; Homo sapiens; ATAC-seq
iPSC-CMs were washed twice with ice-cold PBS and manually scraped using cold PBS on ice. [transposase protocol] iPSC-derived cardiomyocytes were processed using the Active Motif ATAC-Seq Kit (53150 ATAC-Seq Kit, Active Motif, Carlsbad, CA, USA) following the manufacturer's directions. Briefly, approximately 100,000 scraped cells in PBS were pelleted by centrifugation at 500 g for 5 min. Cell pellets were resuspended in 100 μl cold ATAC Lysis Buffer. This solution was pelleted by centrifugation at 500 g for 5 min at 4 °C. Lysis buffer was removed and isolated nuclei were resuspended in 50 μl transposition mix. The tagmentation reaction was carried out at 37 °C for 30 min in a thermomixer set at 800 rpm. Transposed DNA was purified following the manufacturers recommendation and resuspended in 35 μl elution buffer, and stored at −20 °C. Paired-end ATAC-seq library preparation was performed on four individuals, in time and treatment balanced batches, following the Active Motif ATAC-Seq kit manufacturer's directions, and amplified for 14 cycles. Libraries were then purified and bioanalyzed to determine library quality. One sample was collected for each time, treatment, and individual for a total of twelve samples per individual. Libraries for each individual (n = 12) were quantified by qPCR before being pooled and run on an Illumnia Nextseq 2000, 50 bp PE reads in 4 treatment and time balanced batches.