Antibodies and reagents
Plasmids and siRNAs
Cell culture and transfection
SILAC labeling
Protein extraction and trypsin digestion
HPLC fractionation
Kcr peptide enrichment
LC-MS/MS analysis
Database searching and protein quantification
Bioinformatics analysis
Immunoprecipitation and Western blotting
Purification of recombinant proteins
GST pull-down assay
Detection of ssDNA
Immunofluorescence staining and confocal microscopy
DNA-protein binding assay
Electrophoretic mobility shift assay
Colony formation assay
Flow cytometry
Statistical analysis
Cells were harvested and washed twice with ice-cold phosphate-buffered saline (PBS) before they were lysed in NETN buffer (100 mM NaCl, 50 mM tris-HCl, 1 mM EDTA, 0.5% NP-40) supplemented with protease inhibitor cocktail (Protease Inhibitor Cocktail Set III; Calbiochem) and histone deacetylase (HDAC) inhibitor [50 mM nicotinamide (NAM) and 3 μM trichostatin A (TSA)] on ice for 30 min followed by centrifugation at 1000g for 10 min at 4°C. The supernatant was discarded, and the pellet was collected as nuclear fraction samples.