Illumina NovaSeq 6000 paired end sequencing; ATAC-seq of a K562 cell line model with a patient-based t(3;8) translocation
ATAC-seq of a K562 cell line model with a patient-based t(3;8) translocation
100.000 K562 cells were lysed in lysis buffer (0.30 M sucrose, 10 mM Tris pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.1% NP40, 0.15 mM Spermine, 0.5 mM Spermidine, 2 mM 6AA), adapted to reduce mitochondrial DNA contamination.   Immediately after lysis, nuclei were spun at 500g for 8 minutes at 4째C. After pelleting the nuclei, we the nuclei were resuspended in Tn5 transposase reaction mix (25 ul 2X TD buffer, 2.5 ul Tn5 transposase, and 22.5 ul nucleasefree water). The transposition reaction was performed at 37째C for 30 minutes. Immediately after the transposition reaction, DNA was purified using a Qiagen MinElute kit.  The transposed library was PCR amplified using Nextera primers. The PCR reaction was subsequently cleaned up using AMPureXP beads.