| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rat monoclonal anti-mouse CD45, APC/Cyanine7, 30-F11 | Biolegend | Cat# 103116; RRID: AB_312981 |
| Rat monoclonal anti-mouse/human CD11b, PerCPCyanine5.5, M1/70 | Biolegend | Cat# 101228; RRID:AB_893233 |
| Armenian hamster monoclonal anti-mouse CD11c, Brilliant Violet 421, N418 | Biolegend | Cat# 117330; RRID:AB_11219593 |
| Mouse monoclonal anti-mouse CD64, PE, X54-5/7.1 | Biolegend | Cat# 139304; RRID:AB_10612740 |
| Mouse monoclonal anti-mouse CD64, Brilliant Violet 605, X54-5/7.1 | Biolegend | Cat# 139323; RRID:AB_2629778 |
| Rat monoclonal anti-mouse Ly6C, Brilliant Violet 786, HK1.4 | Biolegend | Cat# 128041; RRID:AB_2565852 |
| Rat monoclonal anti-mouse Ly6G, FITC, 1A8 | Biolegend | Cat# 127606; RRID:AB_1236488 |
| Rat monoclonal anti-mouse I-A/I-E, Brilliant Violet 510, M5/114.15.2 | Biolegend | Cat# 107636; RRID:AB_2561397 |
| Rat monoclonal anti-mouse CD170 (Siglec F), APC, S17007L | Biolegend | Cat# 155508; RRID:AB_2750237 |
| Rat monoclonal anti-CD45R/B220, BUV395, RA3-6B2 | BD Biosciences | Cat# 563793; RRID:AB_2738427 |
| Rat monoclonal anti-CD45R/B220, PE, RA3-6B2 | BD Biosciences | Cat# 553090; RRID:AB_394620 |
| Mouse monoclonal anti-rat CD90 / mouse CD90.1 (Thy-1.1), Brilliant Violet 510, OX-7 | Biolegend, | Cat# 202535; RRID:AB_2562643 |
| Rabbit monoclonal anti-FGFR1OP (EPR9929) | Abcam | Cat# ab156013 |
| Rabbit polyclonal anti-EpCAM | Abcam | Cat# ab71916; RRID:AB_1603782 |
| Rabbit monoclonal anti-Lysozyme (EPR2994(2)) | Abcam | Cat# ab108508;b RRID:AB_10861277 |
| Rat monoclonal anti-Tubulin (YL1/2) | Abcam | Cat# ab6160; RRID:AB_305328 |
| Rat monoclonal anti-Brdu (BU1/75 (ICR1)) | Abcam | Cat# ab6326; RRID:AB_305426 |
| Rabbit monoclonal anti-Iba-1/AIF-1 (E4O4W) | Cell Signaling Technology | Cat# 17198S; RRID:AB_2820254 |
| Rabbit monoclonal anti-OLFM4 (D6Y5A) | Cell Signaling Technology | Cat# 39141; RRID:AB_2650511 |
| Rabbit polyclonal anti-phospho-Histone H3 (Ser10) | Cell Signaling Technology | Cat# 9701; RRID:AB_331535 |
| Mouse monoclonal anti-β-catenin, cl.14 | BD Biosciences | Cat# 610153; RRID:AB_397554 |
| Goat polyclonal anti- S100a9 | R&D Systems | Cat# AF2065; RRID:AB_2184263 |
| Rabbit monoclonal anti-non-muscle Myosin IIA (EPR22933-9) | Abcam | Cat# 238131; RRID:AB_2924880 |
| Mouse anti-gamma-tubulin (cl.GTU-88) | MilliporeSigma | Cat# T6557; RRID:AB_477584 |
| Donkey anti-Mouse IgG (H+L), Alexa Fluor 488 | Thermo Fisher Scientific | Cat# A-21202; RRID:AB_141607 |
| Donkey anti-Mouse IgG (H+L), Alexa Fluor 594 | Thermo Fisher Scientific | Cat# A-21203; RRID:AB_141633 |
| Donkey anti-Rabbit IgG (H+L), Alexa Fluor Plus 594 | Thermo Fisher Scientific | Cat# A-32754; RRID:AB_2762827 |
| Goat anti-Rabbit IgG (H+L), Alexa fluor 647 | Thermo Fisher Scientific | Cat# A-21245; RRID:AB_2535813 |
| Donkey anti-Rabbit IgG (H+L), Alexa fluor 647 | Thermo Fisher Scientific | Cat# A-31573; RRID:AB_2536183 |
| Donkey anti-Rat IgG (H+L), Alexa Fluor 594 | Thermo Fisher Scientific | Cat# A-21209; RRID:AB_2535795 |
| Mouse monoclonal anti-Phospho-Myosin Light Chain 2 (Ser19) | Cell Signaling Technology | Cat# 3675; RRID:AB_2250969 |
| Rabbit monoclonal anti-Myosin Light Chain 2 (D18E2) | Cell Signaling Technology | Cat# 8505; RRID:AB_2728760 |
| Rabbit monoclonal anti-GAPDH (14C10; HRP conjugate) | Cell Signaling Technology | Cat# 3683; RRID:AB_1642205 |
| Mouse monoclonal anti-GAPDH (1E6D9) | Proteintech | Cat# 60004-1-Ig; RRID:AB_2107436 |
| anti-mouse IgG, HRP linked | Cell Signaling Technology | Cat# 7076; RRID:AB_330924 |
| anti-rabbit IgG, HRP linked | Cell Signaling Technology | Cat# 7074; RRID:AB_2099233 |
| Mouse monoclonal anti-beta actin (C4) HRP | Santa Cruz Biotechnology | Cat# sc-47778 HRP; RRID:AB_2714189 |
| Anti-FLAG | Millipore Sigma | Cat# F3165; RRID:AB_259529 |
| Chemicals, peptides, and recombinant proteins | ||
| Alexa Fluor 647 Phalloidin | Thermo Fisher Scientific | Cat# A22287 |
| Tamoxifen | MilliporeSigma | Cat# T5648 |
| (Z)-4-Hydroxytamoxifen | MilliporeSigma | Cat# H7904 |
| Fluorescein isothiocyanate–dextran | MilliporeSigma | Cat# 46944 |
| Trilogy | MilliporeSigma | Cat# 920P |
| ProLong Glass Antifade Mountant | Life Technologies | Cat# P36930 |
| Fluoromount | Millipore Sigma | Cat# F4680 |
| Paraformaldehyde (32%) | Electron Microscopy Sciences | Cat# 15714 |
| Tissue-Plus O.C.T. compound | Fisher HealthCare | Cat# 4585 |
| Matrigel | Corning | Cat# 354234 |
| Hoechst 33258 | Invitrogen | Cat# H3569 |
| 4’,6-Diamidino-2-Phenylindole Dihydrochloride (DAPI) | MilliporeSigma | Cat# D9542 |
| RIPA buffer (10x) | Cell Signaling Technologies | Cat# 9806 |
| Protease/phosphatase inhibitor cocktail (100x) | Cell Signaling Technologies | Cat# 5872 |
| Collagenase/Dispase | Roche | Cat# 10269638001 |
| DNase I | Roche | Cat# 11284932001 |
| Dextran sulfate sodium salt, colitis grade (36,000 – 50,000) | MP Biomedicals | Cat# 0216011080 |
| DSS for colitis | TbD Labs. | N/A |
| Collagenase from Clostridium histolyticum | MilliporeSigma | Cat# C5138 |
| DL-Dithiothreitol | MilliporeSigma | Cat# 646563 |
| Percoll | Cytiva | Cat # 17089101 |
| Agar | MilliporeSigma | Cat# A7921 |
| Formalin solution, neutral buffered, 10% | MilliporeSigma | Cat# HT501128 |
| Corn oil | MilliporeSigma | Cat# C8267 |
| Xylenes | MilliporeSigma | Cat# 247642 |
| 2-propanol | MilliporeSigma | Cat# 190764 |
| Trizma base | MilliporeSigma | Cat# T1503 |
| Y-27632 | R&D Systems | Cat# 1254 |
| TrypLE Express | Gibco | 12605-010 |
| Lipofectamine 2000 Transfection Reagent | Thermo Fisher Scientific | Cat# 11668027 |
| Puromycin dihydrochloride | MilliporeSigma | Cat# P9620 |
| PenStrep | Gibco | Cat# 15140-122 |
| 7AAD Viability Staining | Biolegend | Cat# 420404 |
| 1M HEPES Buffer | Corning | Cat# 25-060-Cl |
| Beta-Mercaptoethanol | Sigma | Cat# M-7522 |
| Bovine Serum Albumin (BSA) | Rockland | Cat# BSA-1000 |
| EDTA, 0.5M | Corning | Cat# 46-034-Cl |
| Glutamax (100x) | Gibco | Cat# 35050-061 |
| MEM Nonessential amino acids (100x) | Corning | Cat# 25-025-Cl |
| Nuclease-free water | Invitrogen | Cat# AM9937 |
| PBS (1x) | Leinco | Cat# P364 |
| RPMI 1640 | Sigma | Cat# R8758-1L |
| Sodium Pyruvate 100mM | Corning | Cat# 25-000-Cl |
| Triton X-100 | Sigma | Cat# T8787 |
| Tween 20 | Fisher Bioreagents | Cat# BP337-500 |
| Ultra-Pure BSA | Thermo Fisher | Cat# AM2616 |
| 10x Tris/Glycine Buffer | Biorad | Cat# 1610734 |
| 10x Tris/Glycine/SDS Buffer | Biorad | Cat# 1610732 |
| Tris Buffered Saline (TBS), 10x solution | Fisher bioreagents | Cat# BP2471-1 |
| Protein Assay Reagent A | Biorad | Cat# 500-0113 |
| Protein Assay Reagent B | Biorad | Cat# 500-0114 |
| Protein Assay Reagent S | Biorad | Cat# 500-0115 |
| 0.05% Trypsin-EDTA | Gibco | Cat# 25300-054 |
| Collagenase Type I | Gibco | Cat# 17100-017 |
| DMEM/F12 | Millipore Sigma | Cat# D6421 |
| Polybrene | Millipore Sigma | Cat# H-9268 |
| Critical commercial assays | ||
| RNeasy Plus Mini Kit | QIAGEN | Cat # 74134 |
| IntestiCult Intestinal Organoid Growth Medium | STEMCELL Technologies | Cat # 06005 |
| SuperSignal West Pico PLUS Chemiluminescent Substrate | Thermo Fisher Scientific | Cat# 34577 |
| Restore Western Blot Stripping Buffer | Thermo Fisher Scientific | Cat# 21059 |
| RNAscope Wash Buffer Reagents | ACDBio | Cat# 310091 |
| RNAscope Target Retrieval Reagents | ACDBio | Cat# 322000 |
| RNAscope H2O2 & Protease Plus Reagents | ACDBio | Cat# 322330 |
| RNAscope 2.5 HD Detection Reagent - Red | ACDBio | Cat# 322360 |
| LIVE/DEAD™ Fixable Aqua Dead Cell Stain Kit, for 405 nm excitation | Life Technologies | Cat# L34957 |
| QIAPrep Spin Miniprep Kit | Qiagen | Cat# 27104 |
| Monarch DNA Gel Extraction Kit | New England BioLabs | Cat# T1020S |
| Gibson Assembly Cloning Kit | New England BioLabs | Cat# E5510S |
| BD Pharmingen APC BrdU kit | BD Biosciences | Cat# 552598 |
| Chromium Next GEM Single Cell 3’ Kit v3.1 | 10x Genomics | PN-1000268 |
| Chromium Next GEM Chip G Single Cell Kit | 10x Genomics | PN-1000120 |
| Dual Index Kit TT Set A | 10x Genomics | PN-1000215 |
| Deposited data | ||
| Microarray of small intestine | This paper | GEO: GSE194311 |
| RNAseq of small intestine crypts | This paper | GEO: GSE195515 |
| RNAseq of spheroids | This paper | GEO: GSE195515 |
| scRNAseq of small intestine crypts | This paper | GEO: GSE194312 |
| scRNA-seq datasets on Crohn’s disease (CD) and Ulcerative Colitis (UC) | Kong et al.7 Smillie et al.37 | Broad Single Cell Portal: SCP18847 and SCP25935 (https://portals.broadinstitute.org/single_cell) |
| Western blot raw data | This paper | DOI: 10.17632/bry9hw4p4h.1 |
| Experimental models: Cell lines | ||
| Caco-2 colorectal adenocarcinoma cells | ATCC | Cat# HTB37 |
| L-WRN | Miyoshi and Stappenbeck28; ATCC | Cat# CRL-3276 |
| Caco2 cells expressing C-terminally or N-terminally expressed FLAG-tagged FGFR1OP | This paper | Colonna lab |
| Caco2 cells expressing FGFR1OP or control shRNA | This paper | Colonna lab |
| Caco2 cells co-expressing FGFR1OP or control shRNA and either non activated or activated NMII RLC | This paper | Colonna lab |
| Fgfr1opfl/fl, Fgfr1opfl/+ and Fgfr1opcKO small intestinal spheroid and organoid cell lines | This paper | Colonna lab |
| 293T | ATCC | CRL-3216 |
| Phoenix-Ampho packaging cell line | Dr. Gary Nolan, Stanford | N/A |
| 2.4G2 | ATCC | Cat# HB-197 |
| Experimental models: Organisms/strains | ||
| B6NTac; B6N-A<tm1Brd>Fgfr1op<tm1a(EUCOMM)Hmgu>/Cnrm | EMMA | EM:04776 |
| B6.Cg-Tg(Vil1-cre)1000Gum/J | Madison et al.57 | JAX# 021504 |
| Vil-CreERT2 | el Marjou et al.58 | JAX# 020282 |
| B6.129P2-Lgr5tm1(cre/ERT2)Cle/J (Lgr5-EGFP-IRES-creERT2) | Barker et al.3 | JAX# 008875 |
| B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J (Rosa-LSL-tdTomato) | Madisen et al.59 | JAX# 007909 |
| C57BL/6J | Jackson Laboratories | JAX# 000664 |
| Oligonucleotides | ||
| RNAscope Probe Mm-Fgfr1op-02 | ACDBio | Cat # 585401 |
| Recombinant DNA | ||
| pCMV3-mFGFR1OP-Flag | SinoBiological | Cat# MG5A4380-CF |
| pCMV3-mFGFR1OP-Flag | SinoBiological | Cat# MG5A4380-NF |
| shERWOOD UltramiR Lentiviral Inducible shRNA target gene set for gene FGFR1OP (pZIP-TRE3G-ZsGreen-Puro vectors ULTRA-3199095 and TLNSU4300) | Transomic technologies | Cat# TLHSU2333 |
| pMXs-IRES-Puro Retroviral Expression Vector | Cell Biolabs, Inc. | Cat# RTV-014 |
| pLVX-EF1a-IRES-mCherry | Clonetech Laboratories, Inc. | No. 631987 |
| psPAX2 | Didier Trono | RRID:Addgene_12260 |
| pCMV-VSV-G | Stewart et al.67 | RRID:Addgene_8454 |
| Software and algorithms | ||
| GraphPad Prism | GraphPad | https://www.graphpad.com/features |
| R 4.4 | The R Foundation | https://www.r-project.org RRID: SCR_001905 |
| Rstudio | The R Foundation | https://posit.co RRID: SCR_000432 |
| CellRanger v6.0.1 | 10xGenomics | https://www.10xgenomics.com/products/single-cell-gene-expression |
| Seurat v4.0.1 | Hao et al.63 | https://satijalab.org/seurat/ |
| Python 3.10 | Python Software Foundation | https://www.python.org RRID: SCR_008394 |
| Imaris V8.3 | Bitplane | RRID: SCR_007370 |
| CellSense | Olympus | https://www.olympus-lifescience.com/en/software/cellsens/ |
| Zen (Blue edition) | Carl Zeiss Microscopy GmbH | https://www.micro-shop.zeiss.com/en/us/softwarefinder/software-categories/zen-blue/ |
| Zen (Black edition) | Carl Zeiss Microscopy GmbH | https://www.micro-shop.zeiss.com/en/us/softwarefinder/software-categories/zen-black/ |
| Metascape | Zhou et al.55 | https://metascape.org |
| FlowJo (v10) | TreeStar | https://www.flowjo.com/solutions/flowjo/ |
| Photoshop | Adobe | https://www.adobe.com/products/catalog.html |
| ImageJ/Fiji | Schindelin et al.60 | https://imagej.net/software/fiji/ RRID: SCR_002285 |
| PEAKS Studio 10 Plus | Bioinfomatic Solutions | https://www.bioinfor.com |
| Scaffold Q+S | Proteome Software | https://www.proteomesoftware.com |
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