GSM6257304: PSEN1-A79V replicate 3 [ATAC-seq]; Homo sapiens; ATAC-seq
ATAC-seq transposition experiments were performed as previously described on 50,000 cells in NDC, PSEN1_A79V, PSEN2_N141I, and APP_V717I hiPSC-derived neurons (replicates, n=3) using the Illumina Nextera DNA Sample Preparation Kit (Illumina, catalog no. 15028523) and the QIAGEN MinElute PCR Purification Kit (QIAGEN, catalog no. 28004). ATAC-seq libraries were generated from transposed DNA using the Kapa Biosystems Real-Time Library Amplification Kit (Kapa Biosystems, catalog no. 07959028001) as recommended by the manufacturer, monitoring amplification by qPCR and stopping the reaction when all samples reached a fluorescence amplification intensity between standards 1 and 3. ATAC-seq libraries were then further purified using the QIAGEN MinElute PCR Purification Kit and sequenced at the UC San Diego IGM sequencing core on an Illumina HiSeq 4000 platform generating paired-end, 50-bp reads with an average of 25 million reads per sample.