| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-SCGBA1 (Clone 394324) | R and D Systems | Cat#MAB4218 RRID: AB_2183286 |
| Anti-acetylated alpha-tubulin (Clone 6-11B-1) | Thermo Fisher | Cat#32-2700 RRID: AB_2533073 |
| Anti-MUC5AC AF700 (Clone45M1) | Novus | Cat#NBP2-32732AF700 RRID: AB_2894883 |
| Anti-CCL20 (Polyclonal) | Abcam | Cat#ab224188 RRID: AB_2894878 |
| Anti-CSF3 AF594 (Clone CSF3/900) | Novus | Cat#NBP2-47934AF594 RRID: AB_2933966 |
| Anti-NP (SARS-CoV) | Center for Therapeutic Antibody Development at Icahn School of Medicine at Mount Sinai | NP-1C7 |
| Anti-cytokeratin 5 AF594 (Polyclonal) | Novus | Cat#NBP2-61931AF594 RRID: AB_2933967 |
| Anti-mouse IgG2b AF555 | Thermo Fisher | Cat#A-21147 RRID: AB_2535783 |
| Anti-rabbit IgG AF555 | Biolegend | Cat#406412 RRID: AB_2563181 |
| Anti-rat IgG AF488 | Thermo Fisher | Cat#A-11006 RRID: AB_2534074 |
| Anti-NP (SARS-CoV-2; Polyclonal) | Novus | Cat#NB100-56576 RRID: AB_838838 |
| Anti-Spike (SARS-CoV-2; Polyclonal) | Novus | Cat#NBP2-24808AF647 RRID: AB_2933968 |
| Anti-cytokeratin 5 (Clone EP1601Y) | Abcam | Cat#ab52635 RRID: AB_869890 |
| Bacteria and virus strains | ||
| SARS-COV-2 (USA/WA1-2020) | BEI Resources | NR-52281 |
| SARS-COV-2 (Beta variant B.1.351) | Gift from Dr. Andy Pekosz. | N/A |
| SARS-COV-2 (Delta variant B.1.617.2) | Obtained from Dr. Viviana Simon | Mount Sinai Pathogen Surveillance program |
| SARS-COV-2 (Omicron variant B.1.1.529, BA.1) | Obtained from Dr. Viviana Simon | Mount Sinai Pathogen Surveillance program |
| Biological samples | ||
| Human lung tissue | This study | N/A |
| Chemical, peptides, and recombinant proteins | ||
| Advanced DMEM/F12 | Thermo Fisher | Cat#12634-028 |
| Fetal Bovine Serum | Thermo Fisher | Cat#50-753-2978 |
| Penicillin streptomycin (PS) | Thermo Fisher | Cat#150-70-063 |
| HEPES (1M) | Thermo Fisher | Cat#15-630-080 |
| Red blood cell lysis buffer | Roche | Cat#11814389001 |
| Cultrex growth factor reduced BME type 2 | Trevigen (Rand D Systems) | Cat#3533-010-02 |
| Collagen I Rat Protein | Thermo Fisher | Cat#A1048301 |
| PneumaCult-Ex plus medium | Stemcell | Cat#05040 |
| PneumaCult-ALI medium | Stemcell | Cat#05001 |
| Hydrocortisone | Stemcell | Cat#07926 |
| Heparin solution | Stemcell | Cat#07980 |
| Y-27632 | Abmole | Cat#Y-27632 |
| DNAse I | Sigma | Cat#D4513 |
| Dispase I | Sigma | Cat#4942086001 |
| Collagenase | Sigma | Cat#9C9407 |
| Paraformaldehyde 16% | Thermo Fisher | Cat#28906 |
| Phalloidin ATTO647N | Sigma | Cat#65906 |
| Fluromount-G | Thermo Fisher | Cat#00-4958-02 |
| DAPI | Thermo Fisher | Cat#D1306 |
| Fc Receptor Blocker | Innovex | Cat#NB309 |
| Background buster | Innovex | Cat#NB306 |
| Mouse serum | Jackson ImmunoResearch | Cat#015-000-120 |
| BSA (IgG-Free, Protease-Free) | Jackson ImmunoResearch | Cat#001-000-161 |
| Dimethyl Sulfoxide (DMSO) | Sigma | Cat#67-68-5 |
| Trypsin-EDTA (0.05%) phenol red | Thermo Fisher | Cat#25-300-062 |
| Zombie Aqua™ Fixable Viability Kit | Biolegend | Cat#423101 |
| Zombie Green™ Fixable Viability Kit | Biolegend | Cat#423111 |
| Saponin | Sigma | Cat#S7900-100G |
| Critical commercial assays | ||
| Cytofix/Cytoperm Fixation/Permeabilization solution kit | BD Biosciences | Cat#554714 |
| Direct-zol RNA MicroPrep kits | Zymo research | Cat#R2062 |
| RNase-free DNase set | Qiagen | Cat#79254 |
| Kapa Stranded mRNA-Seq Library Prep kit | Kapa Biosystems | Cat#KK8401 |
| Viral stock protocol | ARTIC | https://artic.network/ncov-2019 |
| Viral-RNA kit | mega-Bio-Tek | Cat#R6874-02 |
| Native Barcoding Expansion kit | ONT | Cat#EXP-NBD104 |
| Deposited data | ||
| Raw data and analyzed data | This study | GEO: GSE225603 |
| Experimental models: Cell lines | ||
| African green monkey (Chlorocebus sabaeus): VeroE6/TMPRSS2 cells | R Rathnasinghe et al.94 | N/A |
| African green monkey (Chlorocebus sabaeus): VeroE6 | ATCC | ATCC CRL-1586, clone E6 |
| Software and algorithms | ||
| Imaris 9.4 | Bitplane | https://imaris.oxinst.com |
| Leica (LAS) X | Leica Microsystems | https://www.leica-microsystems.com/ |
| Adobe Illustrator | Adobe | https://www.adobe.com/products/illustrator.html |
| BD FACSuite Software | BD Biosciences | https://www.bdbiosciences.com/ |
| GraphPad Prism v8 | GraphPad | https://www.graphpad.com/ |
| Flowjo V10.3 | Flowjo LLC | https://www.flowjo.com/ |
| DNAstar | Lasergene | https://www.dnastar.com/software/lasergene/ |
| R (v4.2.0) | The R Foundation | https://www.r-project.org/ |
| ggplot2 (R package v3.3.6) | R package | https://rpkgs.datanovia.com/survminer/index.html |
| ComplexHeatmappackage (v2.12.1) | R package | https://jokergoo.github.io/ComplexHeatmap/ |
| RSEM v1.3.3 | B. Li and Colin N. Dewey.95 | https://github.com/deweylab/RSEM/releases/tag/v1.3.3 |
| Bowtie | Langmead, B. et al.96 | http://bowtie-bio.sourceforge.net/index.shtml |
| FastQC | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ | N/A |
| MultiQC | Ewels, P., et al.97 | N/A |
| BBDuk tool | BBMap download | SourceForge.net | https://sourceforge.net/projects/bbmap/ |
| DESeq2 | R package Love, M.I. et al.98 |
N/A |
| SVAseq | R package | https://doi.org/10.1093/nar/gku864 |
| Reference manager | Mendeley | https://www.mendeley.com/search/ |
| Others | ||
| Greiner CELLSTAR multiwell culture plates (24 wells) | Sigma | Cat#M9312 |
| Corning Transwell polyster membrane cell culture insert (24 wells, 0.4 μm) | Sigma | Cat#3470 |
| Tissue-Tek OCT Compound | Thermo Fisher | Cat#4583 |
| Slides | Denville Scientific | Cat#M1021 |
| Cover Glass | Thermo Scientific | Cat#152450 |
| Schematic and Graphical abstract images | Servier Medical Art | https://creativecommons.org/licenses/by/3.0/ |
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