| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rat anti Sca1 (177228) | R&D systems | Cat #: BAM1226, RRID:AB_2070040 |
| Rabbit anti Anxa1 | Invitrogen | Cat #: PA5-27315, RRID:AB_2544791 |
| Mouse anti E-cadherin (36/E-cadherin) | BD Transduction Laboratory | Cat #: 610181, RRID:AB_397580 |
| Rat anti E-cadherin (ECCD-2) | Thermo Fisher Scientific | Cat #: 13-1900, RRID: AB_86571 |
| Rat anti b1 integrin (MB1.2) | Millipore | Cat #: MAB1997, RRID: AB_2128202 |
| Rabbit anti FAK | Millipore | Cat #: 06-543, RRID: AB_310162 |
| Rabbit anti pSrc (Tyr416) | Cell Signaling Technology | Cat #: 2101, RRID: AB_331697 |
| Rabbit anti YAP | Cell Signaling Technology | Cat #: 4912, RRID:AB_2218911 |
| Rabbit anti Lysozyme (EC.3.2.1.17) | Dako | Cat #: A0099, RRID:AB_2341230 |
| Rabbit anti Ki67 | Abcam | Cat #: ab15580, RRID: AB_443209 |
| Rabbit anti MUC2 (H-300) | Santa Cruz | Cat #: sc-15334, RRID: AB_2146667 |
| Rabbit anti Carbonic Anhydrase II (H-70) | Santa Cruz | Cat #: sc-25596, RRID: AB_2065996 |
| Goat anti Lrig1 | R&D systems | Cat #: AF3688, RRID: AB_2138836 |
| Rabbit anti EpCAM | B.N.G. Giepmans | Schnell et al., 2013 |
| Rat anti Reg3b antibody | R&D systems | Cat #: MAB5110, RRID: AB_2178585 |
| Goat and Trop2 antibody | R&D systems | Cat #: AF1122, RRID: AB_2205662 |
| Alexa Flour 488 Donkey anti Rat IgG (H+L) | Thermo Fisher scientific | Cat #: A-21208, RRID: AB_141709 |
| Alexa Flour 555 Donkey anti Rat IgG (H+L) | Abcam | Ab-150154 |
| Alexa Flour 488 Donkey anti Rabbit IgG (H+L) | Thermo Fisher scientific | Cat #: A-21206, RRID: AB_141708 |
| Alexa Flour 555 Goat anti Mouse IgG2a (H+L) | Thermo Fisher scientific | Cat #: A-21137, RRID: AB_2535776 |
| Alexa Flour 488 Donkey anti Goat IgG (H+L) | Thermo Fisher scientific | Cat #: A-11055, RRID: AB_142672 |
| Anti-Mouse EpCAM APC (G8.8) | eBioscience | Cat #: 17-5791-80, RRID: AB_1659714 |
| Anti-Mouse CD31 PE-Cyanine7 (390) | eBioscience | Cat #: 25-0311-81, RRID: AB_469615 |
| PECy7 Rat anti-Mouse CD45 (30-F11) | BD PharMingen | Cat #: 561868, RRID: AB_10893599 |
| PE/Cy5 anti-mouse Ly6A/E (Sca1) (D7) | Biolegend | Cat #: 108109, RRID: AB_313346 |
| Biological Samples | ||
| Biopsies from human colon | Herlev hospital | O.H. Nielsen |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Dextran Sulfate Sodium (DSS) | MP Biomedicals | 0216011090 |
| Tamoxifen | Sigma | T5648 |
| Growth factor reduced Matrigel | Corning | 356231 |
| Cellmatrix Type I-A | Nitta Gelatin | 631-00651 |
| human EGF | Peprotech | AF-100-15 |
| murine Noggin | Peprotech | 250-38 |
| human Noggin | Peprotech | 120-10C |
| mouse R-spondin1 | R&D systems | 3474-RS |
| human R-spondin1 | Sino | 11083-H08H |
| murine Wnt3a | Cell guidance systems | GFM77 |
| Bovine Serum Albumin | Sigma | A9576 |
| Nicotinamide | Sigma | 72340 |
| Prostaglandin E2 | Sigma | P5640 |
| Y-27632 dihydrochloride | Sigma | Y0503 |
| Jagged-1 | Anaspec | AS-61298 |
| CHIR99021 | Stemgent | 04-0004 |
| Doxycycline | Sigma | D9891 |
| C3 toxin (Rho inhibitor I) | Cytoskeleton | CT04-A |
| Mevastatin | Sigma | M2537 |
| Cytochalasin D | Sigma | C8273 |
| FAK inhibitor (in vitro) | Tocris | PF573228 |
| Src inhibitor (in vitro) | Sigma | Dasatinib |
| FAK inhibitor (in vivo) | Selleckchem | PND-1186 |
| Src inhibitor (in vivo) | Selleckchem | Saracatinib |
| Verteporfin | Sigma | SML0534 |
| Jagged-1 | Anaspec | AS-61298 |
| Indomethacin | Sigma | I7378 |
| Puromycin | Sigma | P8833 |
| 4-hydroxytamoxifen | Sigma | H6278 |
| Critical Commercial Assays | ||
| Lipofectamin 2000 | Thermo Fisher Scientific | 11668027 |
| Hematoxylin QS | Vector | H-3404 |
| Eosin Y Solution Aqueous | Sigma | HT110232 |
| Vector Red Alkaline Phosphatase (Red AP) Substrate Kit | Vector | SK-5100 |
| Alexa Fluor 647 Phalloidin | Molecular Probes | A22287 |
| PureLink RNA Micro-scale kit | Invitrogen | 12183016 |
| Superscript III reverse transcriptase | Invitrogen | 18080093 |
| Deposited Data | ||
| Raw and analyzed data from homeostatic and repairing epithelium | This paper | E-MTAB-5249 |
| Raw and analyzed data from adult and fetal culture | This paper | E-MTAB-5246 |
| Raw and analyzed data from Collagen and Matrigel culture | This paper | E-MTAB-5247 |
| Experimental Models: Cell Lines | ||
| Wnt3a-expressing HEK293 cells | H. Clevers | n/a |
| Experimental Models: Organisms/Strains | ||
| Rosa26mT/mG | A.G. Botton | Muzumdar et al., 2007 |
| tetO-YAP S127A | F. Camargo | Camargo et al., 2007 |
| Yap1fl/fl | D.J. Pan | Zhang et al., 2010 |
| Villin-CreERT2 | S. Robine | el Marjou et al., 2004 |
| Tazfl/fl | S. Piccolo | Azzolin et al., 2014 |
| RAG2−/− | Taconic | C57BL/6NTac |
| Rosa26-rtTAM2 | Jackson Laboratory | Stock No: 006965 |
| Oligonucleotides | ||
| sgRNA targeting exon 15 of Apc (GCACTCAAAACGCTTTTGA) | B.K. Koo | Schwank et al., 2013 |
| Recombinant DNA | ||
| Cas9 | Schwank et al., 2013 | Addgene #41815 |
| Software and Algorithms | ||
| NDP.view2 | Hamamatsu | U12388-01 |
| ImageJ | NIH image | version 2.0.0-rc-41/1.50d |
| Adobe Photoshop CS6 | Adobe | version 13.0.6 x64 |
| Gene set enrichment analysis | http://software.broadinstitute.org/gsea/index.jsp | n/a |
| Other | ||
| Costar 48 Well Clear TC-Treated Multiple Well Plates | Corning | 3548 |
| Histoacryl Topical Skin Adhesive | B.Braun/TissueSeal | TS1050071FP |
| OCT compound | CellPath | KMA-0100-00A |
| Disposable microtome blades, S35 | Feather | 207500000 |
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