GSM8388854: C413, T cell lymphoma, biol rep 2 [ATAC-Seq]; Mus musculus; ATAC-seq
Snap frozen tumor tissue was lyzed in homogenization buffer. Nuclei were pelleted by centrifugation (5 min, 4°C, 350 rcf). Nuclei were resuspended in homogenization buffer and gradients of iodixanol solution were used to obtain the band containing the nuclei at the 30 – 40% iodixanol interface after centrifugation (20 min, 4°C, 3000 rcf, break off). Nuclei were diluted in ATAC-RSB-Tween buffer and counted. 50,000 nuclei per sample were centrifuged (10 min, 500 rcf, 4°C) and resuspended in ATAC-seq Reaction Mix. Reactions were incubated (37°C, 30 min, 1000 rpm). After incubation, Binding Buffer (Qiagen MinElute PCR Purification kit) was added. A cleaning protocol using the MiniElute PCR Purification kit was performed according to the manufacturer and samples were eluted in Elution Buffer. Purified DNA was amplified using qPCR with index primers in 2 rounds of amplification using the NEBNext® High-Fidelity 2X PCR Master Mix (New England Biolabs). Following 2 times SPRI beads purification, library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). For sequencing, samples were diluted and pooled into NGS libraries in equimolar amounts.