title: GSM4587171: Prog_treated_with_BAZ2B_Donor_A; Homo sapiens; ATAC-seq
library_construction_protocol: Samples were purified using a Zymo DNA clean and concentrator kit and eluted in 22 uL ultrapure water. Appropriate sample indexing for 6-plex sequencing on an Illumina NextSeq were chosen for each library and the samples were amplified for 5 cycles to incorporate the sequencing adapters. A qPCR reaction was then performed to determine the optimal additional number of amplification cycles required for each sample to minimize PCR duplication, and each library was amplified for the appropriate number of additional cycles. No libraries exceeded a total of 11 PCR cycles. After library amplification, the samples were again purified with the Zymo kit and eluted in 22 uL ultrapure water. Next, each library was run on a Novex-TBE 4-20% PAGE 10-well non-denaturing gel and subsequently stained with SYBR Gold. The gel was imaged and fragments within the range of 100-1000 bp were excised from the gel for each library. The libraries were recovered from the PAGE gel fragments using electroelution using D-tubes. The libraries were finally purified from the recovered TBE buffer using an Isopropanol/Acetate precipitation. Following the final purification of the libraries, quality control was done by perfoming a Bioanalyzer and KAPA qPCR library quantification assay. This allowed the determination of accurate library concentrations, after which the libraries were pooled, prepped for sequencing on an Illumina Nextseq 500/550 by standard methods using a 75 cycle High-output kit.