ATAC-seq of mus musculus: non-senescent B cell lymphoma
50,000 cells from each time point of the senescence time course (two biological replicates) were collected, washed in 1 in PBS and centrifuged at 500g at 4C for 5min. Nuclei were extracted by incubating cells in nuclear extraction buffer (containing 10mM Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuging at 500g at 4C for 5min. The supernatant was carefully removed by pipetting, and the transposition was performed by resuspending nuclei in 50l of Transposition Mix containing 1 TD Buffer (Illumina) and 2.5l Tn5 (Illumina) for 30min at 37C. DNA was extracted using a Qiagen MinElute kit. Libraries were produced by PCR amplification (12-14 cycles) of tagmented DNA using a NEB Next High-Fidelity 2 PCR Master Mix (New England Biolabs). Library quality was assessed using an Agilent Bioanalyzer 2100. Paired-end sequencing was performed in an Illumina Hiseq 4000. 60 million reads per library were required for downstream analyses.