KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| rabbit anti-p16 | Abcam | Cat#ab108349; RRID: AB_10858268 |
| rabbit anti-p16 | Proteintech | Cat#10883–1-AP; RRID: AB_2078303 |
| rabbit anti-HMGB1 | Abcam | Cat#ab79823; RRID: AB_1603373 |
| rabbit anti-HMGN2 | Cell Signaling Technology | Cat#9437S; RRID: AB_10949505 |
| mouse anti-RPLP0 | Sigma | Cat#SAB1402899; RRID: AB_10738968 |
| rabbit anti-UCHL1 | Cell Signaling Technology | Cat#13179S; RRID: AB_2798141 |
| mouse anti-VAT1 | Santa Cruz Biotechnology | Cat#sc-515705 |
| rabbit anti-LAMP1 | Cell Signaling Technology | Cat#9091; RRID: AB_2687579 |
| mouse anti-γ-H2AX | Sigma Millipore | Cat#05–636-I; RRID: AB_2755003 |
| rabbit anti-p21 | Abcam | Cat#ab109199; RRID: AB_10861551 |
| mouse anti-p21 | Santa Cruz Biotechnology | Cat#sc-6246; RRID: AB_628073 |
| rabbit anti-53BP1 | Novus Biologicals | Cat#NB100304; RRID: AB_10003037 |
| mouse anti-Lamin B1 | Cell Signaling Technology | Cat#68591; RRID: AB_2799751 |
| rat anti-Tubulin | Abcam | Cat#ab6160; RRID: AB_305328 |
| rabbit anti-Actin | Sigma-Aldrich | Cat#A2103; RRID: AB_476694 |
| mouse anti-GAPDH | Thermo Fisher Scientific | Cat#MA5–15738; RRID: AB_10977387 |
| Alexa Fluor 488 goat anti-mouse IgG | Thermo Fisher Scientific | Cat#A11029; RRID: AB_2534088 |
| Alexa Fluor 594 goat anti-rabbit IgG | Thermo Fisher Scientific | Cat#A11037; RRID: AB_2534095 |
| Alexa Fluor 405 goat anti-rat IgG | Abcam | Cat#ab175673; RRID: AB_2893021 |
| Alexa Fluor 647 goat-anti-mouse IgG | Thermo Fisher Scientific | Cat#A32728; RRID: AB_2633277 |
| Alexa Fluor 488 goat-anti-rabbit IgG | Thermo Fisher Scientific | Cat#A32731; RRID: AB_2633280 |
| Alexa Fluor 680 goat anti-Mouse IgG | Thermo Fisher Scientific | Cat#A21058; RRID: AB_2535724 |
| Alexa Fluor 790 goat anti-Rabbit IgG | Thermo Fisher Scientific | Cat#A11369; RRID: AB_2534142 |
| Bacterial and virus strains | ||
| Biological samples | ||
| Chemicals, peptides, and recombinant proteins | ||
| TPCK-treated Trypsin | Worthington | Cat#LS003740 |
| Trypsin GOLD TMT10plex Mass Tags | Promega Thermo Scientific | Cat#V5280 Cat#90110 |
| L-LYSINE:2HCL - Unlabeled | Cambridge Isotope Lab | Cat#ULM-8766-PK |
| L-ARGININE:HCL - Unlabeled | Cambridge Isotope Lab | Cat#ULM-8347-PK |
| L-LYSINE:2HCL (4,4,5,5-D4, 96–98%) | Cambridge Isotope Lab | Cat#DLM-2640–0.5 |
| L-ARGININE:HCL (13C6, 99%) | Cambridge Isotope Lab | Cat#CNLM-2265-H-0.25 |
| L-LYSINE:2HCL (13C6, 99%; 15N2, 99%) | Cambridge Isotope Lab | Cat#CNLM-291-H-1 |
| L-ARGININE:HCL (13C6, 99%; 15N4, 99%) | Cambridge Isotope Lab | Cat#CNLM-539-H-1 |
| DMEM for SILAC | Thermo Fisher Scientific | Cat#A33822 |
| HyClone Dialyzed heat-inactivated FBS | Cytiva | Cat#SH3007903HI |
| Palbociclib | Sigma-Aldrich | Cat#PZ0383 |
| Rapamycin | Thermo Fisher Scientific | Cat#AAJ62473MF |
| Doxorubicin | Thermo Fisher Scientific | Cat#D419325MG |
| Barasertib | Selleck Chemicals | Cat#AZD1152-HQPA |
| Hoechst 33342 | Thermo Fisher Scientific | Cat#H1399 |
| DAPI (4’,6-Diamidino-2-Phenylindole, Dilactate) | Thermo Fisher Scientific | Cat#D3571 |
| Lysotracker Red DND-99 | Thermo Fisher Scientific | Cat#L7528 |
| Critical commercial assays | ||
| Pierce BCA Protein Assay Kit | Thermo Scientific | Cat#23225 |
| Sep-Pak 50mg C18 Cartridges | Waters | Cat##054955 |
| High pH Revered-phased Peptide Fractionation Kit | Thermo Scientific | Cat#84868 |
| Senescence β-Galactosidase Staining Kit | Cell Signaling Technology | Cat#9860 |
| Direct-zol™ RNA Microprep Kit | Zymo Research | Cat#R2063 |
| Click-iT™ EdU Alexa Fluor™ 647 Flow Cytometry Assay Kit | Thermo Fisher Scientific | Cat#C10424 |
| CellTrace™ CFSE Cell Proliferation Kit | Thermo Fisher Scientific | Cat#C34554 |
| Deposited data | ||
| All Proteomics raw files and spectral searches | This paper | PRIDE:PXD033332 |
| All RNAseq raw files | This paper | GEO: GSE208348 |
| Experimental models: Cell lines | ||
| hTERT RPE1 | Stearns Lab (Stanford) | RRID: CVCL_4388 |
| Primary human fetal lung fibroblasts | Cell Applications | Cat#506–05f |
| Experimental models: Organisms/strains | ||
| Oligonucleotides | ||
| Recombinant DNA | ||
| Software and algorithms | ||
| FlowJo | BD Biosciences, https://www.flowjo.com/solutions/flowjo | RRID: SCR_008520 |
| FIJI | https://imagej.net/software/fiji/ | RRID: SCR_002285 |
| MaxQuant | Mann Lab | N/A |
| Python - Jupyter Notebooks | Anaconda | N/A |
| Other | ||