GSM8619607: ATAC Biol rep 2; KO, CX3CR1+ TEX; Mus musculus; ATAC-seq
Cells were lysed using cold ATAC buffer (10 mM Tris–HCl pH 7.5, 10 mM NaCl and 3 mM MgCl2 in UltraPure DNase/RNase-free distilled water (Thermo Fisher Scientific)) comprising NP40 (Millipore-Sigma, 0.1 %), Tween-20 (Millipore-Sigma, 0.1 %) and digitonin (Promega, 0.01 %) for 3 min. Nuclei were pelleted at 500 g for 10 min 4 °C and resuspended in Transposition Mix (Tagment DNA buffer and Tn5 Tagment DNA TDE1 Enzyme from Illumina, PBS, UltraPure DNase/RNase-free distilled water, 0.001 % digitonin, 0.1 % Tween-20). Enzymatic transposition of DNA was achieved by incubation at 37 °C for 30 min at 1000 rpm. DNA was purified using the DNA Clean and Concentrator-5 Kit (Zymo Research). Fragments were barcoded in a PCR reaction with unique Adapter sequences using the NEBNext Ultra II Q5 2x Master Mix (New England Biolabs). Library concengtrations were quantified using the NEBNext Libary Quant Master Mix Kit (New England Biolabs) by qPCR. Individual samples were further amplified to obtain unified library concentrations.