GSM9490626: PB14; Mus musculus; ATAC-seq
ATAC-seq was performed using the Omni-ATAC protocol. Briefly, 50,000 dissociated cells from normal pineal gland or pineal tumor tissue were washed in cold 1× PBS and pelleted by centrifugation. Cell pellets were lysed in ice-cold lysis buffer containing Tris-HCl, NaCl, MgCl₂, NP-40, Tween-20, and digitonin, followed by incubation on ice. Nuclei were washed in resuspension buffer and pelleted prior to transposition. DNA was purified after transposition using the Qiagen MinElute Reaction Cleanup Kit according to the manufacturer's instructions. Purified nuclei were subjected to transposition using Tn5 transposase at 37 °C for 30 minutes with agitation. Transposed DNA fragments were PCR-amplified using Nextera i5 common and i7 indexed adapters. Libraries were size-selected by double-sided magnetic bead purification to remove primer dimers and large fragments (>1,000 bp). Library quality and insert size distribution were assessed using Agilent BioAnalyzer, TapeStation, or Fragment Analyzer systems. Libraries were quantified by PicoGreen dsDNA assay or low-pass sequencing and sequenced as paired-end 100-bp reads on an Illumina NovaSeq 6000.