KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| APC anti-KIT | eBioscience | Cat#17-1171-82 RRID:AB_469430 |
| ASCL1 [EPR19840] | Abcam | Cat#ab211327 RRID:AB_2924270 |
| Beta III Tubulin (TUBB3)/TUJ1 | Abcam | Cat#ab18207 RRID:AB_444319 |
| Beta III Tubulin (TUBB3)/TUJ1: for IF costains | Biolegend | Cat#801201 RRID:AB_2728521 |
| CD11B | Abcam | Cat# ab133357 RRID:AB_2650514 |
| CD3 | Abcam | Cat#ab5690 RRID:AB_305055 |
| CGRP | Sigma | Cat#C8198 RRID:AB_259091 |
| Chromogranin A (CHGA) | Novus Biologicals | Cat#NB120-15160 RRID:AB_789299 |
| TRP63 (P63) | R&D Systems | Cat#599-AF1916 RRID:AB_2207174 |
| KIT | Cell Signaling Technology | Cat#3074 RRID:AB_1147633 |
| HES1 | Cell Signaling Technology | Cat#11988 RRID:AB_2728766 |
| LHX2 | Sigma | Cat#ABE1402 RRID:AB_2722523 |
| mCherry (tdTomato) | Sigma | Cat#AB356481 RRID:AB_2861426 |
| MKI67: for mouse IHC | BD Biosciences | Cat#556003 RRID:AB_396287 |
| NCAM1 | R&D Systems | Cat#AF2408 RRID:AB_442152 |
| NEUROD1 [EPR4008]: for mouse IHC | Abcam | Cat#ab109224 RRID:AB_10861489 |
| NEUROD1: for IF | Cell Signaling Technology | Cat#4373 RRID:AB_10549071 |
| NEUROD1: for IF costains | R&D Systems | Cat#AF2746 RRID:AB_2149217 |
| NKX2-1 (TTF1) | Abcam | Cat#ab76013 RRID:AB_1310784 |
| Pan-Cytokeratin (Pan-CK) | Thermo Fisher Scientific | Cat#BS1712R RRID:AB_10855057 |
| POU2F3 | Sigma | Cat#HPA019652 RRID:AB_1855585 |
| S100B | Abcam | Cat#ab4066 RRID:AB_304258 |
| SOX2 | Cell Signaling Technology | Cat#3728 RRID:AB_2194037 |
| SOX9: for IF | Cell Signaling Technology | Cat#82630 RRID:AB_2665492 |
| SOX9: for IHC | Abcam | Cat#ab185966 RRID:AB_2728660 |
| Synaptophysin (SYP) | Cell Signaling Technology | Cat#36406S RRID:AB_2799098 |
| UCHL1 | Sigma | Cat#HPA00593 |
| YAP1 | Cell Signaling Technology | Cat#14074 RRID:AB_2650491 |
| Peroxidase AffiniPure Donkey Anti-Rabbit IgG (H+L) | Jackson ImmunoResearch | Cat#711-035-152; RRID: AB_10015282 |
| Peroxidase AffiniPure Goat Anti-Mouse IgG1, Fcg Subclass 2b Specific | Jackson ImmunoResearch | Cat#115-035-205; RRID: AB_2338513 |
| CD45-532: for Spatial Transcriptomics | Novus Biologicals | Cat#NBP2-34528AF532 RRID:AB_2864384 |
| TUBB3-594: for Spatial Transcriptomics | Biolegend | Cat#657408 RRID:AB_2565285 |
| KI67-647: for Spatial Transcriptomics | Cell Signaling Technology | Cat#12075 RRID:AB_2728830 |
| Bacterial and Virus Strains | ||
| Ad5-CGRP-Cre | University of Iowa Viral Vector Core Facility | Cat# VVC-Berns-1160 |
| Ad5-CMV-Cre | University of Iowa Viral Vector Core Facility | Cat# VVC-U of Iowa-5 |
| CellTag Barcode Library V1 | Addgene | RRID:Addgene_115643 |
| Biological Samples | ||
| Human ONB tissue | Duke University Hospital | N/A |
| Mouse tissues | This paper | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Normal Goat Serum | Jackson Immunoresearch | Cat#005-000-121 |
| Normal Donkey Serum | Jackson Immunoresearch | Cat#017-000-001 |
| 10% Neutral Buffered Formalin | Fisher Scientific | Cat#22-110-869 |
| Ethanol (200 Proof) | VWR | Cat#TX89125172DUK |
| Hydrogen Peroxide | Fisher Scientific | Cat#H325-500 |
| Tween-20 | Fisher Scientific | Cat#BP337-500 |
| ACK Lysing Buffer | Thermo Fisher Scientific | Cat#A10492 |
| Collagenase Type 1A | Sigma | Cat#C9891 |
| Collagenase, Type 4 | Worthington Biochemical | Cat#LS004186 |
| Dispase | Worthington Biochemical | Cat#LS02104 |
| DMSO | Fisher Scientific | Cat#BP231-100 |
| CaCl2 | Sigma | Cat#C5670 |
| MEM | Thermo Fisher Scientific | Cat#11095080 |
| Formaldehyde (37% by weight) | Thermo Fisher Scientific | Cat#BP531-500 |
| HBSS-free media | Thermo Fisher Scientific | Cat#14175 |
| HBSS without calcium or magnesium | Thermo Fisher Scientific | Cat#14025 |
| Trypsin-EDTA | Thermo Fisher Scientific | Cat#25200-072 |
| Leibovitz’s L15 media | Thermo Fisher Scientific | Cat#11415-064 |
| Fetal Bovine Serum (FBS) | Sigma | Cat#12303C |
| DNase | Sigma | Cat#D4527 |
| Sucrose | VWR | Cat#97061-428 |
| SYTO 13 nuclear dye | Thermo Fisher Scientific | Cat#S7575 |
| Methimazole (MMZ) | Sigma | Cat#M8506 |
| DNase I | Stem Cell Tech | Cat#07900 |
| Papain | Stem Cell Tech | Cat#07465 |
| Neurocult media | Stem Cell Tech | Cat#05700 |
| 4% paraformaldehyde | Sigma Aldrich | Cat#158127 |
| OCT | VWR | Cat#25608-930 |
| Antigen Unmasking Solution, Citrate Based | Vector Laboratories | Cat# H-3300-250 |
| BSA | VWR | Cat#97061-422 |
| Triton X-100 | Chem Impex | Cat#1279 |
| Hoescht stain | Thermo Fisher | Cat#62249 |
| Vectashield | Vector Laboratories | Cat#H-1000 |
| TAT-Cre Recombinase | EMD Millipore | Cat#SCR508 |
| SPRIselect | Beckman Coulter Life Sciences | Cat#B23317 |
| Advanced DMEM/F-12 | Fisher Scientific | Cat#12-634-028 |
| L-glutamine | Thermo Fisher | Cat#35050079 |
| Penicillin-Streptomycin (Pen-strep) | Thermo Fisher | Cat# 15140163 |
| Y27632 (Rho-kinase inhibitor) | MedChemExpress | Cat# HY-10071 |
| TrypLE | Thermo Fisher | Cat#12604013 |
| DNeasy DNA Isolation Kit | Qiagen | Cat#69506 |
| GoTaq | Promega | Cat#M7123 |
| Polybrene | Santa Cruz | Cat#sc-134220 |
| PRR Matrigel, Phenol Red-Free | University of Utah | N/A |
| L-WRN conditioned organoid media | University of Utah | N/A |
| Critical Commercial Assays | ||
| DAB Peroxidase (HRP) Substrate Kit | Fisher Sci | Cat#NC9276270 |
| VECTASTAIN ABC Kit (Rabbit IgG) | Vector Laboratories | Cat#PK-4001 |
| SignalStain Boost IHC Detection Reagent (HRP, Rabbit) | Cell Signaling Technology | Cat#8114 |
| SignalStain Antibody Diluent | Cell Signaling Technology | Cat#8112 |
| Mouse on Mouse (M.O.M) Basic Kit | Vector Laboratories | Cat#BMK-2202 |
| TSA Fluorescein System | Akoya Biosciences | Cat#NEL701A001KT |
| Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 | 10X Genomics | Cat#PN-1000268 |
| Chromium Single Cell Controller | 10X Genomics | Cat#PN-120263 |
| Chromium Next GEM Chip G Single Cell Kit | 10X Genomics | Cat# 1000120 |
| GeoMx Human Whole Transcriptome Atlas Probe Mix | NanoString | Cat#GMX-RNA-NGS-HuWTA-4 |
| APC selection kit | Stem Cell Tech | Cat#17667 |
| 10X Magnetic Separator | Fisher Scientific | Cat#NC1469069 |
| Plasmid Plus Mega Kit | Qiagen | Cat#12981 |
| Deposited Data | ||
| Single cell RNA-Seq normal unlesioned mouse OE | Horgue et al. 2022 | GEO: GSE185168 |
| Single cell RNA-seq lesioned mouse OE dataset | Ko et al, 2023 | GEO: GSE224894 |
| ASCL1 conserved targets by ChIP-seq | Borromeo et al. 2016 | GEO: GSE69398 |
| NEUROD1 conserved targets by ChIP-seq | Borromeo et al. 2016 | GEO: GSE69398 |
| NEUROD1 ChIP-seq data from RPM mouse tumors | Olsen et al. 2021 | GEO: GSE155692 |
| Single cell RNA-seq RPM ONB | This study | GEO Superseries: GSE244123 (Subseries GSE244122) |
| Single cell RNA-seq RPMA ONB | This study | GEO Superseries: GSE244123 (Subseries GSE244122) |
| Single cell RNA-seq RPM and RPMA GBC-derived allografts | This study | GEO Superseries: GSE244123 (Subseries GSE244119) |
| Spatial transcriptomics human ONB | This study | GEO Superseries: GSE244123 (Subseries: GSE244117) |
| Single cell RNA-seq human ONB-B | This study | GEO Superseries: GSE244123 (Subseries: GSE248746) |
| RNA-seq from 19 human ONBs | Classe et al., 2018 | GEO: GSE118995 |
| RNA-seq from 21 prostate neuroendocrine carcinomas | Labrecque et al., 2019 | GEO: GSE126078 |
| RNA-seq from 16 small cell lung cancers | Rudin et al., 2012 | EGAS00001000334 |
| RNA-seq from 20 medulloblastomas | Northcott et al., 2017 | N/A |
| RNA-seq from 3 normal human OEs | Olender et al., 2016 | GEO: GSE80249 |
| Single cell RNA-seq from a human ONB (ONB-A) | Zunitch et al., 2023 | GEO: GSE166612 |
| Single cell RNA-seq atlas from 7 human patients | Finlay et al., 2022; Durante et al., 2020; Oliva et al., 2022 | GEO: GSE139522; GEO: GSE184117 |
| GitHub and Zenodo deposit of all source code | This study | GitHub: https://github.com/Goldstein-Lab/Finlay_and_Ireland_et_al_mouse_ONB
Zenodo: DOI: 10.5281/zenodo.10829939 |
| Experimental Models: Organisms/Strains | ||
| Mouse: Rb1fl/fl;Trp53fl/fl;MycT58ALSL/LSL (RPM) | Trudy G. Oliver, Duke University, Mollaoglu et al, 2017 | The Jackson Lab RRID:IMSR_JAX:029971 |
| Mouse: Rb1fl/fl;Trp53fl/fl; MycT58ALSL/LSL;Ascl1fl/fl (RPMA) | Trudy G. Oliver, Duke University, Olsen et al, 2021 | N/A |
| Mouse: Rb1fl/fl;Trp53fl/fl;MycT58ALSL/LSL-Cas9 (RPM-Cas9 or RPM-GFP) | Trudy G. Oliver, Duke University, Ireland et al, 2020 | N/A |
| Mouse: C.B-Igh-1b/GbmsTac-Prkdcscid-Lystbg N7 (Scid/Beige) | Gift of Zachary C. Hartmann, Duke University | Taconic RRID:IMSR_TAC:CBSCBG |
| Mouse: B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J (R26R-Ai9 tdTomato Reporter) | The Jackson Laboratories | The Jackson Lab RRID:IMSR_JAX:007909 |
| Mouse: Rb1fl/fl;Trp53fl/fl;Rbl2fl/fl | Schaffer et al., 2010 | RRID: MMRRC 043692-UCD |
| Cell Line: HEK 293T/17 | ATCC | Cat#CRL-11268 RRID:CVCL_1926 |
| Tumor organoids: KIT+ GBCs from Rb1fl/fl;Trp53fl/fl; MycT58ALSL/LSL;Ascl1fl/fl (RPMA) (RPMA) and Rb1fl/fl;Trp53fl/fl; MycT58ALSL/LSL (RPM) olfactory epithelium | This study | N/A |
| Software and Algorithms | ||
| Graphpad Prism | Graphpad Software | www.graphpad.com/scientific-software/prism/ |
| Quantum GX2 mCT Software | PerkinElmer | N/A |
| Analyze 11.0 | AnalyzeDirect | https://analyzedirect.com/ |
| Python (v3.8.8) | Python Software | https://www.python.org/ |
| Scanpy (v1.9.1) | Wolf et al., 2018 | https://scanpy.readthedocs.io/en/stable/ |
| scvi-tools (v0.17.4) | Gayoso et al., 2022 | scvi-tools.org |
| otscomics (v0.1.0) | Huizing et al., 2022 | https://ot-scomics.readthedocs.io/en/latest/ |
| Osn package (v0.0.1) | Tsukahara et al., 2021 | https://github.com/dattalab/Tsukahara_Brann_OSN/tree/main/osn |
| 10X Genomics Cell Ranger v7.0.0 | Zheng, et al. 2017 | https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov |
| Gene Set Enrichment Analysis (GSEA) | Broad Institute, and the Regents of the University of California | http://software.broadinstitute.org/gsea/index.jsphttp://software.broadinstitute.org/gsea/index.jsp |
| Enrichr | Kuleshov et al., 2016 | http://amp.pharm.mssm.edu/Enrichr/http://amp.pharm.mssm.edu/Enrichr/ |
| Seurat | Butler et al., 2018; Stuart and Butler et al., 2019 | https://satijalab.org/seurat/https://satijalab.org/seurat/ |
| R Statistical Programming | The R Foundation | www.r-project.orgwww.r-project.org |
| edgeR (v3.40.2) | Robinson et al., 2010 | https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| BioRender | BioRender.com | https://app.biorender.com |
| Velocyto (v0.17.17) | La Manno et al. 2018 | https://velocyto.org/ |
| UCSC Genome Browser | Kent et al. 2002 | https://genome.ucsc.edu/ |
| scVelo (v0.2.5) | Bergen et al. 2020 | https://pypi.org/project/scvelo/ |
| NanoStringNCTools (v1.6.1) | Aboyoun et al., 2021 | https://bioconductor.org/packages/release/bioc/html/NanoStringNCTools.html |
| GeomxTools (v3.2.0) | Ortogero et al. 2023 | https://www.bioconductor.org/packages/release/bioc/html/GeomxTools.html |
| GeoMxWorkflows (v1.4.0) | Reeves et al. 2023 | https://www.bioconductor.org/packages/release/workflows/html/GeoMxWorkflows.html |
| CellTagR | Kong et al. 2020 | https://github.com/morris-lab/CellTagR |
| TCGAbiolinks (v2.25.3) | Colaprico et al., 2015 | https://www.bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html |
| ImageJ (v2.3.0) | Reuden et al. 2017 | https://imagej.net/software/imagej2/ |
| NCI GDC Data Portal | National Cancer Institute (NCI) | https://gdc.cancer.gov/access-data/gdc-data-portal |