GSM5831057: PBS +CNV; Mus musculus; ATAC-seq
Sorted CX3CR1+ cells were used for scATAC-seq and nuclei isolation was performed according to the protocol of 10x Genomics. Briefly, isolated cells were centrifuged at 300xg for 5 min at 4°C and then resuspended in ice-cold PBS+0.04% BSA. The cell lysis was performed for 4 minutes on ice by adding 45μl lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P-40, 0.01% Digitonin, and 1% BSA). After lysis, 50μl ice-cold wash buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, and 1% BSA) were added and then centrifuged at 500 × g for 5 min at 4 °C. After one more wash, the washed nuclei were counted and used for the transposase reaction.  After removing the supernatant, the pellet was resuspended in 7 ml 1x Nuclei Buffer (10x Genomics) and 2 ml of the nuclei suspension was taken for evaluation (nuclei quality control and determining nuclei concentration). The library was constructed according to the Chromium Single Cell ATAC Reagent Kits protocol (10x Genomics).