KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
|
| ||
| Rabbit mAb anti-phospho-Rb (Ser807/811) | Cell Signaling Technology | Cat# 8516; RRID: AB_11178658 |
| Mouse mAb anti-Rb (4H1) | Cell Signaling Technology | Cat# 9309; RRID: AB_823629 |
| Rabbit mAb anti-cleaved caspase3 (Asp175) | Cell Signaling Technology | Cat# 9579; RRID: AB_10897512 |
| Rabbit mAb anti-c-Myc (D84C12) | Cell Signaling Technology | Cat# 5605; RRID: AB_1903938 |
| Mouse mAb anti-β-Actin (8H10D10) | Cell Signaling Technology | Cat# 3700; RRID: AB_2242334 |
| Rabbit mAb anti-Phospho-Akt (Ser473) | Cell Signaling Technology | Cat# 9271; RRID: AB_329825 |
| Mouse mAb anti-Akt (pan) (40D4) | Cell Signaling Technology | Cat# 2920; RRID: AB_1147620 |
| Rabbit mAb anti-Phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) | Cell Signaling Technology | Cat# 4370; RRID: AB_2315112 |
| Mouse mAb anti-p44/42 MAPK (Erk1/2) (L34F12) | Cell Signaling Technology | Cat# 4696; RRID: AB_390780 |
| Rabbit polyclonal Ab anti-GAPDH | Santa Cruz Biotechnology | Cat# sc-25778; RRID: AB_10167668 |
| Mouse mAb anti-PCNA (PC10) | Santa Cruz Biotechnology | Cat# sc-56; RRID: AB_628110 |
| Rabbit mAb anti-Rb | Abcam | Cat# ab181616; RRID: AB_2848193 |
| Rabbit mAb anti-c-Myc (Y69) | Abcam | Cat# ab32072; RRID: AB_731658 |
| IgG (H + L) Highly Cross-Adsorbed Goat anti-Rabbit, Alexa Fluor™ Plus 488 | Invitrogen | Cat# A32731; RRID: AB_2633280 |
| IgG (H + L) Highly Cross-Adsorbed Goat anti-Mouse, Alexa Fluor™ Plus 488 | Invitrogen | Cat# A32723; RRID: AB_2633275 |
| IgG (H + L) Highly Cross-Adsorbed Goat anti-Mouse, Alexa Fluor™ 568 | Invitrogen | Cat# A11031; RRID: AB_144696 |
| IgG (H + L) Cross-Adsorbed Goat anti-Rabbit Alexa Fluor™ 488 | Invitrogen | Cat# A11008; RRID: AB_143165 |
| IgG (H + L) Highly Cross-Adsorbed Goat anti-Mouse, Alexa Fluor™ 568 | Invitrogen | Cat# A11031; RRID: AB_144696 |
| Goat-anti-mouse IR Dye 800CW | LI-COR Biosciences | Cat# 926-32210; RRID: AB_621842 |
| Goat-anti-rabbit IR Dye 680RD | LI-COR Biosciences | Cat# 926-68071; RRID: AB_10956166 |
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| Chemicals, peptides, and recombinant proteins | ||
|
| ||
| Doxycycline | Sigma-Aldrich | Cat# D9891 |
| 5-Ethynyl-2′-deoxyuridine | Sigma-Aldrich | Cat# 900584 |
| 5-Ethynyl-Uridine | Click Chemistry Tools | Cat# 1261 |
| Palbociclib | Selleck Chemicals | Cat# S1116 |
| Abemaciclib | Selleck Chemicals | Cat# S7158 |
| Ribociclib | Selleck Chemicals | Cat# S7440 |
| Trametinib | Selleck Chemicals | Cat# S2673 |
| EN4 | Selleck Chemicals | Cat# S9807 |
| Bortezomib | MedChem Express | Cat# HY-10227 |
| Ixazomib | MedChem Express | Cat# HY-10453 |
| Carfilzomib | MedChem Express | Cat# HY-10455 |
| Alpelisib | MedChem Express | Cat# HY-15244 |
| Fulvestrant | MedChem Express | Cat# HY-13636 |
| Pictilisib | MedChem Express | Cat# HY-50094 |
| Palbociclib (mice experiment) | MedChem Express | Cat# HY-50767 |
| Chloroquine | MedChem Express | Cat# HY-17589A |
| MG-132 | Calbiochem | Cat# 474790 |
| Epoxomicin | Cayman Chemical | Cat# 134381-21-8 |
| ONX0914 | Cayman Chemical | Cat# 960374-59-8 |
| Celastrol | Cayman Chemical | Cat# 34157-83-0 |
| Omarigliptin | Cayman Chemical | Cat# 1226781-44-7 |
| PMSF | Cayman Chemical | Cat# 329-98-6 |
| Maribavir | Cayman Chemical | Cat# 176161-24-3 |
| MLN9708 (Ixazomib citrate) | Cayman Chemical | Cat# 1201902-80-8 |
| Nafamostat mesylate | Cayman Chemical | Cat# 82956-11-4 |
| N-ethylmaleimide | Cayman Chemical | Cat# 128-53-0 |
| Camostat mesylate | Cayman Chemical | Cat# 59721-29-8 |
| Leupeptin hemisulfate | Cayman Chemical | Cat# 103476-89-7 |
| MG101 | Cayman Chemical | Cat# 110044-82-1 |
| Loxistatin acid | Cayman Chemical | Cat# 76684-89-4 |
| PI1840 | Cayman Chemical | Cat# 1401223-22-0 |
| Aloxistatin | Cayman Chemical | Cat# 88321-09-9 |
| VR23 | Cayman Chemical | Cat# 1624602-30-7 |
| Paritaprevir | Cayman Chemical | Cat# 1221573-85-8 |
| Delanzomib | Cayman Chemical | Cat# 847499-27-8 |
| Oprozomib | Cayman Chemical | Cat# 935888-69-0 |
| Z-FA-FMK | Cayman Chemical | Cat# 197855-65-5 |
| 17β-estradiol pellet (0.36 mg) | Innovative Research of America | Cat# SE-121 |
| 16% Paraformaldehyde | Ted Pella Inc | Cat# NC1537886 |
| Fetal Bovine Serum (FBS) | Gibco | Cat# 10-437-028 |
| Puromycin | Invivogen | Cat# ant-pr-1 |
| Blasticidin | Invivogen | Cat# ant-bl-1 |
| DPBS without Ca2+, Mg2+ | Genesee | Cat# 25-508 |
| Triton X-100 | Millipore Sigma | Cat# T8787 |
| Hoechst 33342 | Thermo Scientific | Cat# 62249 |
| Dimethyl sulfoxide (DMSO) | Millipore Sigma | Cat# D2438 |
| Trypsin-EDTA, 0.25% 1X, phenol red, without Calcium and Magnesium | Genesee | Cat# 25-510 |
| Bovine Serum Albumin (BSA) Protease-free powder | Millipore Sigma | Cat# A3311 |
| Protein G Agarose Beads | Cell Signaling Technology | Cat# 37478 |
| SimplyBlue™ SafeStain | Invitrogen | Cat# LC6060 |
| AFDye 647 Picolyl Azide | Click Chemistry Tools | Cat# 1300 |
| (+)-SODIUM L-ASCORBATE | Millipore Sigma | Cat# A4034 |
| COPPER(II) SULFATE (CuSO4) | Millipore Sigma | Cat# C1297 |
| Halt protease inhibitor cocktail | Thermo Scientific | Cat# 1861279 |
| PhosSTOP | Millipore Sigma | Cat# 4906845001 |
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| Critical commercial assays | ||
|
| ||
| GeneJET Plasmid Miniprep Kit | Thermo Fisher | Cat# K0503 |
| NucleoBond Xtra Midi prep kit | Macherey-Nagel | Cat# 740410.100 |
| PureLink™ RNA Mini Kit | Invitrogen | Cat# 12183018A |
| SuperScript IV VILO Master Mix | Invitrogen | Cat# 11756050 |
| PowerTrack SYBR Green Master Mix | Thermo Fisher | Cat# A46109 |
| ViewRNA ISH Cell Assay | Invitrogen | Cat# QVC0001 |
| ViewRNA Cell Probe Set: E2F1 | Invitrogen | Cat# VA1-12108-VC |
| ViewRNA Cell Probe Set: Cdc25A | Invitrogen | Cat# VA1-15814-VC |
| ViewRNA Cell Probe Set: RB1 | Invitrogen | Cat# VA1-3000151-VC |
|
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| Experimental Models: Cell Lines | ||
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| MCF-7 | ATCC | Cat# HTB-22 |
| CAMA-1 | ATCC | Cat# HTB-21 |
| MDA-MB-157 | ATCC | Cat# HTB-24 |
| MDA-MB-231 | ATCC | Cat# CRM-HTB-26 |
| MDA-MB-468 | ATCC | Cat# HTB-132 |
| T47D | ATCC | Cat# CRL-2865 |
| HCC1428 | ATCC | Cat# CRL-2327 |
| HCC1143 | ATCC | Cat# CRL-2321 |
| HCC1937 | ATCC | Cat# CRL-2336 |
| BT-483 | ATCC | Cat# HTB-121 |
| BT-20 | ATCC | Cat# HTB-19 |
|
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| Deposited Data | ||
|
| ||
| Raw data | Mendeley Data | Mendeley: http://doi.org/10.17632/c47xz5mgp3.1 |
|
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| Experimental models: Organisms/strains | ||
|
| ||
| J:NU mice | The Jackson Laboratory | Cat#007850 |
| Experimental models: Organisms/strains | ||
| gRNA targeting Rb (GUUCGAGGUGAACCAUUAAUGUUUUAGAGCUAUGCU) | Integrated DNA Technologies | N/A |
| gRNA targeting Rb (AAGUGAACGACAUCUCAUCUGUUUUAGAGCUAUGCU) | Integrated DNA Technologies | N/A |
| siRNA targeting CCNE1, sense sequence (GAUCAGCACUUUCUUGAGCAACACC) | Integrated DNA Technologies | N/A |
| siRNA targeting CCNE1, anti-sense sequence (CCCUAGUCGUGAAAGAACUCGUUGUGG) | Integrated DNA Technologies | N/A |
| siRNA targeting CCNE1, sense sequence (AUGCAAAAGGUUUCAGGGUAUCAGT) | Integrated DNA Technologies | N/A |
| siRNA targeting CCNE1, anti-sense sequence (ACUACGUUUUCCAAAGUCCCAUAGUCA) | Integrated DNA Technologies | N/A |
| siRNA targeting CCNE2, sense sequence (CAUUCUGACUUGGAACCACAGAUGA) | Integrated DNA Technologies | N/A |
| siRNA targeting CCNE2, anti-sense sequence (ACGUAAGACUGAACCUUGGUGUCUACU) | Integrated DNA Technologies | N/A |
| siRNA targeting CCNE2, sense sequence (ACGUAAGACUGAACCUUGGUGUCUACU) | Integrated DNA Technologies | N/A |
| siRNA targeting CCNE2, anti-sense sequence (AGUCAGGAACGUAAUAGUAACUUUGUG) | Integrated DNA Technologies | N/A |
| siRNA targeting c-Myc, sense sequence (AUCAUUGAGCCAAAUCUUAAAAAAA) | Integrated DNA Technologies | N/A |
| siRNA targeting c-Myc, anti-sense sequence (UAUAGUAACUCG GUUUAGAAUUUUUUU) | Integrated DNA Technologies | N/A |
| siRNA targeting c-Myc, sense sequence (CGACGAGACCUUCAUCAAAAACATC) | Integrated DNA Technologies | N/A |
| siRNA targeting c-Myc, anti-sense sequence (CUGCUGCUCUGGAAGUAGUUUUUGUAG) | Integrated DNA Technologies | N/A |
|
| ||
| Recombinant DNA | ||
|
| ||
| pLV-DHB (a.a.995–1087)-mVenus-p2a-mCherry-Rb (a.a.886–928)-IRES-blasticidin | Yang et al.33 | RRID: Addgene_126679 |
| pLV-H2B-iRFP670-p2a-mCerulean-Geminin (1–110)-IRES-Neomycin | This paper | |
| pLV-YFP-Rb-IRES-blasticidin | This paper | |
| pLV-YFP-Rb (14 Ser/Thr to Glu)-IRES-puromycin | This paper | |
| pLV-H2B-iRFP670-p2a-YFP-Rb-IRES-blasticidin | This paper | |
| pCW57.1-Cyclin D1-IRES-puromycin | This paper | |
| pCW57.1-Cyclin E1-IRES-puromycin | This paper | |
| pCW57.1-c-Myc-IRES-puromycin | This paper | |
| pCMV-VSV-G | Stewart et al.59 | RRID: Addgene_8454 |
| pRSV-rev | Dull et al.60 | RRID: Addgene_12253 |
| pMDLg/pRRE | Dull et al.60 | RRID: Addgene_12251 |
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| Software and algorithms | ||
|
| ||
| MATLAB | MathWorks | https://www.mathworks.com/ |
| MATLAB Scripts | MathWorks | http://doi.org/10.5281/zenodo.8310175 |
| Image Studio Lite | LI-COR Biosciences | https://www.licor.com/bio/image-studio-lite/ |
| Image Lab 5.2.1 | Bio-Rad | https://www.bio-rad.com/en-us/product/image-lab-software?ID=KRE6P5E8Z |