KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
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| Anti-cyclin D1 | Cell Signaling Technologies | Cat# 55506; RRID: AB_2827374 |
| Anti-Phospho-Histone H2A.X (Ser139) | Cell Signaling Technologies | Cat# 9718; RRID:AB_2118009 |
| Anti-Yap1 | Santa Cruz Biotechnology | Cat# 101199; RRID: AB_1131430 |
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| Bacterial and virus strains | ||
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| Stellar Competent E. coli | Clontech | Cat# 636766 |
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| Chemicals, peptides, and recombinant proteins | ||
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| PND 1186 | Tocris | Cat# 6891 |
| (3-Aminopropyl)trimethoxysilane | Sigma-Aldrich | Cat# 281778 |
| CellTrace Far Red | Invitrogen | Cat# C34572 |
| Cell Mask Deep Red | Invitrogen | Cat# C10046 |
| Cell Mask Orange | Invitrogen | Cat# C10045 |
| Coverslips, 22 mm x 22 mm | Fisher | Cat# 50–189-9787 |
| DMEM-L-glut, high-glucose | Fisher/Mediatech | Cat# MT10–013-CVEA |
| DPBS without Ca Mg | Fisher/Mediatech | Cat# MT21–031-CVEA |
| Trypsin 0.25% | Fisher/Mediatech | Cat# MT25–053CIEA |
| RIPA buffer (150 mM NaCl, 5mM EDTA, 50mM Tris, 1% NP40, 0.5% sodium deoxycholate, 0.1% sodium dodecyl sulfate) | This paper | N/A |
| Janelia Fluor 646 halotag ligand | Promega | Cat# GA1120 |
| Janelia Fluor 549 halotag ligand | Promega | Cat# GA1110 |
| Fugene HD | Promega | Cat# E2311 |
| SNAP-Cell® 505-Star | New England Biolabs | Cat# S9103S |
| SNAP-Cell® TMR-Star | New England Biolabs | Cat# S9105S |
| Polybrene | EMD Millipore | Cat# TR-1003-G |
| PD 0332991 (Palbociclib) | Cayman Chemical | Cat# 16273 |
| Collagen I, rat tail | Corning | Cat# 354236 |
| Glutaraldehyde 70% | Fisher | Cat# 16360 |
| Paraformaldehyde 16% | Fisher | Cat# 15710 |
| calcium-free DMEM powder | US Biological | Cat# 09800 |
| Puromycin Dihydrochloride | Fisher | Cat# A1113803 |
| SYLGARD™ 184 Silicone Elastomer Kit | Dow | Cat# 1673921 |
| Corning™ F12K Medium | Corning | Cat# MT10025CV |
| Chelex 100 | Simga | Cat# C7901 |
| Doxycycline hyclate (dox) | Fisher | Cat# AC446060050 |
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| Critical commercial assays | ||
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| NucleoSpin RNA Purification Kit | Macherey Nagel | Cat# 740955 |
| Pierce™ BCA Protein Assay Kit | Thermo Scientific | Cat# 23225 |
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| Deposited data | ||
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| Imaging data | This paper | Figshare: https://doi.org/10.6084/m9.figshare.22231219 |
| RNA sequencing data | This paper | GEO: GSE227906 |
| Histology analysis | This paper | Figshare: https://doi.org/10.6084/m9.figshare.22231219 |
| Simulation Data | This paper | Zenodo: https://doi.org/10.5281/zenodo.7632621 |
| Dog reference genome NCBI build 3.1, CanFam3.1 | NCBI | https://www.ncbi.nlm.nih.gov/assembIy/GCF_000002285.3/ |
| human protein atlas CDH1 histology | Human Protein Atlas | https://www.proteinatlas.org/ENSG00000039068-CDH1 |
| Allen cell 3D cell viewer | Allen Cell | https://www.allencell.org/3d-cell-viewer.html |
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| Experimental models: Cell lines | ||
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| MDCK | Laboratory of W. James Nelson (Stanford) | RRID: CVCL_0422 |
| HaCaT | Laboratory of Yu-Ying He (University of Chicago) | RRID: CVCL_0038 |
| CACO-2 | ATTC | HTB-37; RRID: CVCL_0025 |
| Mouse Embryonic Fibroblasts (MEF) | Laboratory of Mary Beckerle (University of Utah) | N/A |
| HEK 293T | ATTC | CRL-3216; RRID: CVCL_0063 |
| hTERT-RPE-1 | Laboratory of Wallace Marshall (UCSF) | RRID: CVCL_4388 |
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| Oligonucleotides | ||
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| Primers for cloning and sequencing, see Table S2 | This Paper | N/A |
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| Recombinant DNA | ||
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| pHR1–8.2-delta-R | Laboratory of Marsha Rosner (University of Chicago) | N/A |
| pCMV-VSV-G | Laboratory of Marsha Rosner (University of Chicago) | N/A |
| pLenti-PGK-Neo-PIP-FUCCI | Addgene | RRID: Addgene_118616 |
| pWPT-Stargazin-Halotag | This paper | N/A |
| pLVX-Tre3g-mEmerald-p27–1-176 | This paper | N/A |
| pLVX-Tre3g-snap-p27ck-1–176 | This paper | N/A |
| pLVX-Tre3g-mEmerald-ccnd1 | This paper | N/A |
| pLVX-Tre3g mEmerald-ccnd1 T286A T288A | This paper | N/A |
| pcDNA cyclin D1 HA | Addgene | RRID: Addgene_11181 |
| pLVX-Tre3g mKate2-T2a-12sE1a | This paper | N/A |
| pBabe 12S E1A | Addgene | RRID: Addgene_18742 |
| pLVX-Tre3g | Takara Lenti-X™ Tet-On® 3G Inducible Expression System | Cat# 631363 |
| pLVX-EF1a-Tet3G | Takara Lenti-X™ Tet-On® 3G Inducible Expression System | Cat# 631363 |
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| Software and algorithms | ||
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| ImageJ | National Institutes of Health | https://imagej.nih.gov/ij/Snapgene.com |
| Snapgene Software | GSL Biotech LLC | |
| Metamorph | Molecular Devices | Moleculardevices.com |
| Image analysis code | This paper | https://github.com/Gardel-lab/Devany2023DevCell |
| Simulation code | This paper | https://github.com/falkma/tissueconfinement-simulations |
| Matlab | Mathworks | https://www.mathworks.com/ |