Antibodies and reagents
Plasmids and siRNAs
Cell culture and transfection
SILAC labeling
Nuclear extraction
Protein extraction and trypsin digestion
HPLC fractionation
Kcr peptide enrichment
LC-MS/MS analysis
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
The resulting MS/MS data were processed using MaxQuant with integrated Andromeda search engine (v.1.5.2.8). Tandem mass spectra were searched against human Swiss-Prot database (20,203 sequences) concatenated with reverse decoy database. Trypsin/P was specified as cleavage enzyme allowing up to four missing cleavages. The mass tolerance for precursor ions was set to 20 parts per million in first search and 5 parts per million in main search, and the mass tolerance for fragment ions was set to 0.02 Da. Carbamidomethyl on Cys was specified as fixed modification, and Kcr modification and oxidation on Met were specified as variable modifications. False discovery rate (FDR) was adjusted to <1%, and minimum score for modified peptides was set to >40.