Key Resources Table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-γ-H2AX | Millipore | Cat#05–636, RRID:AB_309864 |
| Rabbit monoclonal anti-phospho-Akt | Cell Signaling Technology | Cat#4058, RRID:AB_331168 |
| Rabbit monoclonal anti-phospho-Erk | Cell Signaling Technology | Cat#4377, RRID:AB_331775 |
| Rabbit monoclonal anti-phospho-Erk | Cell Signaling Technology | Cat#4370, RRID:AB_2315112 |
| Mouse monoclonal anti-Erk | Cell Signaling Technology | Cat#4696, RRID:AB_390780 |
| Rabbit polyclonal anti-phospho-JNK | Cell Signaling Technology | Cat#9251, RRID:AB_331659 |
| Rabbit polyclonal anti-JNK | Cell Signaling Technology | Cat#9252, RRID:AB_2250373 |
| Mouse monoclonal anti-NF-κB | Santa Cruz | Cat#sc-8008, RRID:AB_628017 |
| Rabbit monoclonal anti-phospho-p38 | Cell Signaling Technology | Cat#4631, RRID:AB_331765 |
| Rabbit polyclonal anti-p38 | Cell Signaling Technology | Cat#9212, RRID:AB_330713 |
| Rabbit monoclonal phospho-MK2 | Cell Signaling Technology | Cat#3007, RRID:AB_490936 |
| Rabbit anti-MK2 | Cell Signaling Technology | Cat#3042, RRID:AB_10694238 |
| Rabbit monoclonal anti-phospho-S6 | Cell Signaling Technology | Cat#4856, RRID:AB_2181037 |
| Mouse monoclonal anti-p27 | Santa Cruz | Cat#sc-1641, RRID:AB_628074 |
| Rabbit monoclonal anti-p27 | Cell Signaling Technology | Cat#3686, RRID:AB_2077850 |
| Rabbit polyclonal anti-phospho-Hsp27 | Cell Signaling Technology | Cat#2401, RRID:AB_331644 |
| Mouse monoclonal anti-p53 | Santa Cruz | Cat#sc-263, RRID:AB_628084 |
| Rabbit polyclonal anti-phospho-c-Jun(Ser 73) | Cell Signaling Technology | Cat#9164, RRID:AB_330892 |
| Rabbit monoclonal anti-phospho-c-Jun(Ser 73) | Cell Signaling Technology | Cat#3270, RRID:AB_2129575 |
| Rabbit polyclonal anti-phospho-c-Jun(Ser 63) | Cell Signaling Technology | Cat#9261, RRID:AB_2130162 |
| Rabbit monoclonal anti-c-Jun | Cell Signaling Technology | Cat#9165, RRID:AB_2130165 |
| Rabbit polyclonal anti-phospho-Chk2 | Cell Signaling Technology | Cat#2661, RRID:AB_331479 |
| Mouse monoclonal anti-IκBα | BD Biosciences | Cat#610691, RRID:AB_398014 |
| Mouse monoclonal anti-IκBα | Cell Signaling Technology | Cat#4814, RRID:AB_390781 |
| Mouse monoclonal anti-Cyclin D | Santa Cruz | Cat#sc-20044, RRID:AB_627346 |
| Rabbit polyclonal anti-phospho-Rb | Cell Signaling Technology | Cat#9308, RRID:AB_331472 |
| Mouse monoclonal anti-Cyclin E | Santa Cruz | Cat#sc-247, RRID:AB_627357 |
| Rabbit polyclonal anti-Cyclin A | Santa Cruz | Cat#sc-751, RRID:AB_631329 |
| Mouse monoclonal anti-p21 | Millipore | Cat#05–345, RRID:AB_309684 |
| Rabbit monoclonal anti-p21 | Cell Signaling Technology | Cat#2947, RRID:AB_823586 |
| Rabbit monoclonal anti-p16 | Cell Signaling Technology | Cat#18769, RRID:AB_2935679 |
| Rabbit polyclonal anti-Cyclin B | Santa Cruz | Cat#sc-752, RRID:AB_2072134 |
| Rabbit monoclonal anti-Cyclin B | Cell Signaling Technology | Cat#12231, RRID:AB_2783553 |
| Mouse monoclonal anti-BrdU | BD Biosciences | Cat#555627, RRID:AB_395993 |
| Mouse monoclonal anti-BrdU | Cell Signaling Technology | Cat#5292S, RRID:AB_10548898 |
| Rabbit polyclonal anti-phospho-RPA2(Ser 8) | Cell Signaling Technology | Cat#83745, RRID:AB_2800029 |
| Rabbit monoclonal anti-RPA2 | Cell Signaling Technology | Cat#35869, RRID:AB_2799086 |
| Mouse monoclonal anti-β-tubulin | Sigma-Aldrich | Cat#T7816, RRID:AB_261770 |
| Mouse monoclonal anti-GAPDH | Cell Signaling Technology | Cat#97166, RRID:AB_2756824 |
| Rabbit monoclonal anti-cleaved caspase-3 | BD Biosciences | Cat#559565, RRID:AB_397274 |
| Mouse monoclonal anti-cleaved PARP | BD Biosciences | Cat#558710, RRID:AB_1645431 |
| Rabbit polyclonal anti-Cyclin B | Santa Cruz | Cat#sc-752, RRID:AB_2072134 |
| Mouse monoclonal anti-p21 | Millipore | Cat#05–345, RRID:AB_309684 |
| Rabbit monoclonal anti-cleaved caspase-3 conjugated to Pacific Blue | Cell Signaling Technology | Cat#8788S, RRID:AB_2797665 |
| Rabbit monoclonal anti-cleaved PARP conjugated to Alexa Fluor 647 | Cell Signaling Technology | Cat#6987S, RRID:AB_10858215 |
| Goat polyclonal anti-rabbit conjugated to Alexa Fluor 488 | Invitrogen | Cat#A-11008, RRID:AB_143165 |
| Goat polyclonal anti-rabbit conjugated to Alexa Fluor 647 | Invitrogen | Cat#A-21245, RRID:AB_141775 |
| Goat polyclonal anti-mouse conjugated to Alexa Fluor 647 | Invitrogen | Cat#A-21236, RRID:AB_2535805 |
| IRDye® 680RD Goat anti-Mouse IgG Secondary Antibody | LI-COR Biosciences |
Cat#926–68070, RRID: RRID:AB_10956588 |
| IRDye® 800CW Goat anti-Rabbit IgG Secondary Antibody | LI-COR Biosciences |
Cat#926–32211, RRID:AB_621843 |
| IRDye® 680RD Goat anti-Rabbit IgG Secondary Antibody | LI-COR Biosciences |
Cat#926–68071, RRID:AB_10956166 |
| IRDye® 800CW Goat anti-Mouse IgG Secondary Antibody | LI-COR Biosciences |
Cat#926–32210, RRID:AB_621842 |
| Bacterial and virus strains | ||
| Competent DH5α E. coli | This paper | NA |
| Chemicals, peptides, and recombinant proteins | ||
| DMEM | Corning | 10–013-CV |
| Fetal bovine serum (FBS) | VWR | 97068–085 |
| Penicillin-streptomycin | Gibco | 15070063 |
| RPMI | Gibco | 11875093 |
| EBM-2 endothelial cell growth medium | Lonza | CC-3162 |
| Doxorubicin hydrochloride | Sigma-Aldrich | PHR1789; CAS: 25316–40-9 |
| SP600125 | Sigma-Aldrich | S5567; CAS: 129–56-6 |
| Neocarzinostatin | Sigma-Aldrich | N9162; CAS: 9014–02-2 |
| Cisplatin | Sigma-Aldrich | P4394; CAS: 15663–27-1 |
| Caffeine | Sigma-Aldrich | C0750; CAS: 58–08-2 |
| Phorbol 12-myristate 13-acetate (PMA) | Sigma-Aldrich | P1585; CAS: 16561–29-8 |
| Anisomycin | Sigma-Aldrich | A9789; CAS: 2286276–6 |
| PD98059 | Cell Signaling Technology | 9900; CAS: 167869- 21–8 |
| SB203580 | Tocris | 1202; CAS: 152121- 47–6 |
| Mitoxantrone | Tocris | 4250; CAS: 70476- 82–3 |
| Doxycycline | Clontech | 631311; CAS: 564- 25–0 |
| DMSO | Sigma-Aldrich | D8418; CAS: 67–68-5 |
| 5-bromo-2’-deoxyuridine (BrdU) | ThermoFisher | B23151; CAS: 59–143 |
| 16% Paraformaldehyde | Electron Microscopy Science |
15710; CAS: 30525- 89–4 |
| PBS | GenClone | 25–507B |
| Triton-X 100 | Sigma-Aldrich | T9284; CAS: 9036–19-5 |
| HCS CellMask Blue | ThermoFisher | H32720 |
| Hoechst 33342 | Invitrogen | H3570 |
| Whole Cell Blue | ThermoFisher | 8403502 |
| 5-ethynyl-2’-deoxyuridine (EdU) | ThermoFisher | A10044 |
| ProLong Gold Antifade Mount | ThermoFisher | P36980 |
| Odyssey Blocking Buffer | LI-COR Biosciences |
927–50000 |
| Propidium iodide with RNase A | Cell Signaling Technology | 4087 |
| Tween 20 | AmericanBio | AB02038; CAS: 9005–64-5 |
| PhosSTOP™ tablets | Roche | 4906837001 |
| cOmplete™ ULTRA Tablets, Mini, EDTA-free, EASYpack Protease Inhibitor Cocktail | Roche | 05892791001 |
| Ponceau stain | Sigma-Aldrich | P7170 |
| Intercept blocking buffer | Licor | 927–70001 |
| NewBlot nitrocellulose stripping buffer | Licor | 928–40030 |
| Lipofectamine RNAiMAX | ThermoFisher | 13778150 |
| Opti-MEM | ThermoFisher | 11058021 |
| Lipofectamine 2000 | ThermoFisher | 11668019 |
| Puromycin | InvivoGen | ant-pr-1; CAS: 58–58-2 |
| Hydrochloric acid | Sigma-Aldrich | 258148; CAS: 7647- 01–1 |
| Citric acid | Sigma-Aldrich | C-4540; CAS: 77–929 |
| Sodium phosphate monobasic | Sigma-Aldrich | S0751; CAS: 7558–80-7 |
| Phusion® High-Fidelity PCR Master Mix with HF Buffer | NEB | M0531S |
| NheI-HF® | NEB | R3131L |
| EcoRI-HF® | NEB | R3101L |
| NEBuilder® HiFi DNA Assembly Master Mix | NEB | E2621S |
| Critical commercial assays | ||
| Senescence β-Galactosidase Staining Kit | Cell Signaling Technology | 9860 |
| Click-iT Plus Alexa Fluor 555 Picolyl Azide Toolkit | ThermoFisher | C10642 |
| IL-6 Human ELISA Kit | ThermoFisher | KHC0061 |
| IL-8 Human ELISA Kit | ThermoFisher | KHC0081 |
| BCA assay | ThermoFisher | 23225 |
| CalPhos™ Mammalian Transfection Kit | Clontech | 631312 |
| Experimental models: Cell lines | ||
| Human: U-2 OS (U2OS) | HTS core at the Koch Institute | RRID:CVCL_T429 |
| Human: OVCAR-8 | Laboratory of Dr. Paula Hammond |
RRID:CVCL_1629 |
| Human: NCI-H1299 | ATCC | RRID:CVCL_0060 |
| Human: HUVEC | Lonza | RRID:CVCL_2959 |
| Human: HEK293T | ATCC | RRID:CVCL_0063 |
| Oligonucleotides | ||
| Non-targeting siRNA | Invitrogen | AM4636 |
| Jun #1 siRNA | Life Technologies |
s7658 |
| Jun #2 siRNA | Life Technologies |
s7659 |
| Recombinant DNA | ||
| pAK-Tol2-TRE-JunDN-HA-T2A-GFP (pTREJunDN-HA-T2A-GFP) | This paper | NA |
| pAK-Tol2-TRE-GFP (pTRE-GFP) | This paper | NA |
| pMIEG3-JunDN | Addgene # 40350 | Ref. 156 |
| pCMV-Tol2 | Addgene # 31823 | Ref. 157 |
| pAK-Tol2-TRE-Puro | Addgene # 130259 | NA |
| pSIRV-AP-1-mCherry | Addgene # 118095 | Ref. 158 |
| pUMVC | Addgene # 8849 | Ref. 159 |
| pCMV-VSV-G | Addgene # 8454 | Ref. 159 |
| Software and algorithms | ||
| Fiji distribution of ImageJ | Ref. 160 | https://fiji.sc/ |
| CellProfiler (version 4.0.6) | Ref. 161 | https://cellprofiler.org/ |
| MATLAB (2019b) | MathWorks | https://www.mathworks.com |
| FlowJo (version 10) | BD Biosciences | https://www.flowjo.com/ |
| Python (version 3.7) | Python Software Foundation | https://www.python.org/ |
| N-way Toolbox (version 1.8.0.0) | Ref. 56 | https://www.mathworks.com/matlabcentral/fileexchange/1088the-n-way-toolbox |
| Multi-way VIP | Ref. 58 | Obtained from corresponding authoruponreques |
| Tensor PLSR and PCA code | This paper | https://doi.org/10.5281/zenodo.7927324 |
| ilastik | Ref. 162 | https://www.ilastik.org/ |
| GraphPad Prism (version 8.4.1) | Dotmatics | https://www.graphpad.com/ |
| NIS Viewer | Nikon | https://www.microscope.healthcare.nikon.com/products/software/nis-elements/viewer |
| Image Studio Lite (version 5.2) | LI-COR Biosciences |
https://www.licor.com/bio/image-studio-lite/ |
| Other | ||
| Corning™ BioCoat™ 12mm #1 German Glass Coverslips, Round | Fisher Scientific | 08–774-383 |
| 96 Well Black/Clear Bottom Plate, TC Surface | ThermoFisher | 165305 |