GSM8530726: ATAC_URF_2; Mus musculus; ATAC-seq
To isolate nuclei, liver samples (50 mg) were homogenized in hypotonic sucrose buffer (250 mM sucrose, 10 mM Tris-Hcl pH 7.8, 0.1% Igepal, 3mM MgCl2, 10mM KCl, 0.2 mM Dithiothreitol, 0.5 mM spermidine, protease inhibitor cocktail) in a dounce homogenizer. Homogenate was filtered through a 20 µM filter, spun and washed (10 mM Tris-Hcl pH 7.5, 3 mM MgCl2, 10 mM NaCl, 0.1% tween-20). 50,000 nuclei were included for next steps as described (Korenfeld et al., 2023). Each sample was sequenced at a depth of at least 50X10^6 reads (paired-end). ATAC-seq libraries were prepared using specific DNA Barcodes and Q5 High-Fidelity DNA Polymerase from New England Biolabs. Libraries were amplified using 13 cycles on the thermocycler. PCR-amplified DNA was purified using a MinElute PCR purification kit from Qiagen following manufacturer's instructions. Post amplification libraries were size selected at 150-400nt in length using magnetic AMPure XP beads from Beckman Coulter.