SILAC labeling and quantitative proteomics analysis were performed as previously described (36). Briefly, WT or CDYL KO HeLa cells were grown in DMEM supplemented with 10% FBS and either heavy form 13C615N4-arginine (Arg10) and 13C614N2-lysine (Lys6) or light form 12C614N4-arginine (Arg0) and 12C614N2-lysine (Lys0), respectively. The cells were grown for more than six generations before being harvested to achieve more than 97% labeling efficiency. After that, the cells were further expanded in SILAC medium to desired cell number (5 × 108) in 15 mm–by–150 mm plates.

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