ATM-Dependent and -Independent Dynamics of the Nuclear
Phosphoproteome After DNA Damage

Ariel Bensimon, Alexander Schmidt, Yael Ziv, Ran Elkon, Shih-Ya Wang, David J. Chen, Ruedi Aebersold,* Yosef Shiloh*

*To whom correspondence should be addressed. E-mail: yossih{at}post.tau.ac.il (Y.S.); rudolf.aebersold{at}imsb.biol.ethz.ch (R.A.)

This PDF file includes:

• Fig. S1. Schematic workflow and estimation of signal-to-noise criteria for fold-change filtering.
• Fig. S2. Time course data set analyzed for overrepresented sequence motifs, as well as known kinase-substrate relationships.
• Fig. S3. PPI network of the DDR phosphoproteome obtained with STRING.
• Fig. S4. Full network view of the protein complexes associated with DDR phosphoproteome identified by CORUM analysis.
• Fig. S5. Full network view of the PPI network of the DDR phosphoproteome identified by PPI Spider analysis.
• Fig. S6. Properties of the PPI Spider protein-protein interaction network of the DDR phosphoproteome.
• Fig. S7. pSer²⁹⁹⁶ on ATM, identified by MS/MS and a phosphorylation-specific antibody, is DNA-PK–independent.
• Fig. S8. The S2996A mutation in ATM does not affect ATM-dependent phosphorylations after DNA damage induction.
• Table S1. List of samples (biological replicates) used for the two MasterMaps.
• Table S3. Significant GO terms extracted from DAVID.
• Table S4. DNA damage–responsive phosphorylation sites with a known kinase identified in databases.
• Table S5. Kinase prediction enrichment analysis of phosphorylation sites and the association with Motif-X motifs.
• Table S6. Kinase prediction enrichment analysis coupled to DAVID GO analysis.
• Table S7. Kinase prediction enrichment analysis coupled to CLICK clustering analysis.
• Table S8. DAVID GO analysis of CLICK clusters.
• Table S9. Protein complexes depicted by CORUM in the protein lists obtained in this study.
• Table S10. Effect of the PPI Spider network generation procedure on the analysis of GO term enrichment.
• Table S12. Kinase prediction enrichment analysis of the ATM dependence data set.

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Other Supplementary Material for this manuscript includes the following:

• Table S2. DNA damage–responsive phosphorylation events in the time course data set.
• Table S11. DNA damage–responsive phosphorylation events in the ATM dependence data set.
• Table S13. Complete list of phosphorylation sites identified in this study.
• Table S14. Complete list of phosphopeptides identified in this study.
  

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