KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse Anti-Cytokeratin 14 (clone RCK107) | Abcam | Cat #ab9220; RRID: AB_307087 |
| Rabbit Anti-Cytokeratin 5 | Abcam | Cat #ab53121; RRID: AB_869889 |
| Rabbit Anti-p63 | Fitzgerald | Cat #70R-50620 |
| Mouse Anti-IGFBP2 (C-10) | Santa Cruz | Cat #sc-25285; RRID: AB_2123220 |
| Rabbit Anti-DCAMKL1 | Abcam | Cat #ab31704; RRID: AB_873537 |
| Mouse Anti-alpha Tubulin (acetyl K40) [6–11B-1] | Abcam | Cat #ab24610; RRID: AB_448182 |
| Rabbit Anti-CCSP | Dr. Barry Stripp | n/a |
| Goat Anti-Muc19 | Abcam | Cat #ab121014; RRID: AB_10971842 |
| Mouse Anti-Surfactant protein D [VIF11] (Biotin) | Abcam | Cat #ab15696; RRID: AB_302044 |
| Mouse Anti-Muc5AC (45M1) | Thermo Fisher Scientific | Cat #MA5–12178; RRID: AB_10978001 |
| Rabbit Anti-Aquaporin 5 | Millipore | Cat #AB3559-50UL; RRID: AB_2141915 |
| Mouse Anti-PCNA [PC10] | Abcam | Cat #ab29; RRID: AB_303394 |
| Rabbit Anti-Fibronectin | Abcam | Cat #ab23751; RRID: AB_447656 |
| Mouse Anti-Hop (E-1) | Santa Cruz | Cat #sc-398703; RRID: AB_2687966 |
| Rabbit Anti-Choline kinase alpha | Abcam | Cat #ab88053; RRID: AB_10675356 |
| Mouse Anti-HEXB B chain (D-9) | Santa Cruz | Cat #sc-376781 |
| Rabbit Anti-SPA (H-148) | Santa Cruz | Cat #sc-13977; RRID: AB_661294 |
| Rabbit Anti-SPB (H-300) | Santa Cruz | Cat #sc-13978; RRID: AB_2185370 |
| Rabbit Anti-Prosurfactant Protein C | Millipore | Cat #AB3786; RRID: AB_91588 |
| Mouse Anti-FOXN4 (G-1) | Santa Cruz | Cat #sc-377166 |
| Rabbit Anti-FOXJ1 | Sigma | Cat #AV38038; RRID: AB_1849069 |
| Goat Alexa Fluor 488 Anti-Rabbit IgG | Invitrogen | Cat #A11034; RRID: AB_2576217 |
| Goat Alexa Fluor 555 Anti-Mouse IgG | Invitrogen | Cat #A21424; RRID: AB_141780 |
| Goat Alexa Fluor 555 Anti-Rabbit IgG | Invitrogen | Cat #A21429; RRID: AB_141761 |
| Donkey Alexa Fluor 555 Anti-Goat IgG | Invitrogen | Cat #A21432; RRID: AB_141788 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Protease XIV from Streptomyces griseus | Sigma | Cat #P5147 |
| Deoxyribonuclease I from bovine pancreas | Sigma | Cat #DN25 |
| Minimum Essential Medium Eagle | Sigma | Cat #M8028 |
| Penn/Strep | GIBCO | Cat #15140–122 |
| Fetal Bovine Serum | HyClone | Cat #SH30071.03 |
| EDTA, 0.5M solution, pH 8.0 | American Bio | Cat #ab00502–01000 |
| Collagenase | Worthington | Cat #LS004196 |
| Amphotericin B | HyClone | Cat #SV30078.01 |
| PureCol Bovine Type I Atelo-Collagen Solution | Advanced Biomatrix | Cat #5005-100ML |
| Bronchial epithelial cell growth medium | Lonza | Cat #CC-3170 |
| EpiX Medium | Propagenix | Cat #276–00A-D |
| Airway Differentiation Supplement | Propagenix | https://www.propagenix.com/index.php/research-products |
| Pneumacult ALI Medium | StemCell Technologies, Inc. | Cat #05001 |
| Heparin | StemCell Technologies, Inc. | Cat #07980 |
| Hydrocortisone | StemCell Technologies, Inc. | Cat #07925 |
| 0.05% Trypsin-EDTA | GIBCO | Cat #25300–054 |
| Growth factor-reduced Matrigel | Corning | Cat #356231 |
| Fibronectin bovine plasma | Sigma | Cat #F4759 |
| DMEM High Glucose | GIBCO | Cat #11965–092 |
| Collagenase/Dispase | Roche | Cat #11097113001 |
| Elastase | Worthington | Cat #LS002292 |
| Liberase TM | Sigma | Cat #5401119001 |
| Bovine Serum Albumin | Gemini Bio-Products | Cat #700–100P |
| RNase-Free DNase | QIAGEN | Cat #79254 |
| DAPI | Thermo Fisher Scientific | Cat #62247 |
| Dispase II | GIBCO | Cat #17105041 |
| Critical Commercial Assays | ||
| RNeasy Mini Kit | QIAGEN | Cat #74106 |
| iScript cDNA Synthesis Kit | BioRad | Cat #1708891 |
| iQ SYBR Green | BioRad | Cat #1708882 |
| Chromium Single Cell 3′ Library & Gel Bead Kit v2 | 10x Genomics | Cat #PN-120237 |
| Chromium Single Cell A Chip Kit | 10x Genomics | Cat #PN-120236 |
| Chromium i7 Multiplex Kit | 10x Genomics | Cat #PN-120262 |
| Clariom S Assay, rat | Thermo Fisher Scientific | Cat #902934 |
| Deposited Data | ||
| scRNaseq data | This paper | GEO: GSE145517 |
| Microarray data | This paper | GEO: GSE145516 |
| Experimental Models: Organisms/Strains | ||
| SAS Sprague-Dawley Rattus norvegicus | Charles River | Strain code: 400 |
| Oligonucleotides | ||
| Primers for β-actin, Foxj1, Krt14, Krt5, Muc5ac, Tp63, see Table S1 | This paper | N/A |
| Software and Algorithms | ||
| Seurat (v2.3) | Satija et al., 2015 | https://satijalab.org/seurat/ |
| SCANPY (v1.4) | Wolf et al., 2018 | https://scanpy.readthedocs.io/en/stable/ |
| Bioinfokit | Renesh Bedre, Ph.D. | https://github.com/reneshbedre/bioinfokit |
| ComplexHeatmap (v2.1.0) | Gu et al., 2016 | http://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html |
| DAVID Gene Ontology | Huang et al., 2009a, 2009b | https://david.ncifcrf.gov/ |
| EnhancedVolcano | https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html | |
| MATLAB custom code | Engler et al., 2019 | N/A |
| Transcriptome Analysis Console (TAC) Software | Thermo Fisher Scientific | https://www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-analysis-instruments-software-services/microarray-analysis-software/affymetrix-transcriptome-analysis-console-software.html |
| Other | ||
| Millicell cell culture insert (12mm, 12 μm) | Millipore | Cat #PIXP01250 |
| Falcon permeable support for 24-well plate (0.4 μm) | Corning | Cat #353095 |