| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-SCGBA1 (clone 394324, rat IgG) antibody dilution: 1/250 | R&D Systems | Cat#MAB4218; RRID: AB_2183286 |
| Anti-acetylated-alpha-tubulin (clone 6-11B-1, mouse IgG2b) antibody dilution: 1/250 | Thermo Fisher Scientific | Cat#32-2700; RRID: AB_2533073 |
| Anti-MUC5AC AF700 (clone 45M1, mouse IgG1) antibody dilution: 1/250 | Novus | Cat#NBP2-32732AF700; RRID: AB_2894883 |
| Anti-CCL20 (rabbit polyclonal) antibody dilution: 1/200 | Abcam | Cat#ab224188; RRID: AB_2894878 |
| Anti-CSF3 AF594 (clone CSF3/900, mouse IgG1) antibody dilution: 1/400 | Novus | Cat#NBP2-47934AF594; RRID: AB_2933966 |
| Anti-NP (SARS-CoV) AF488 or AF647 antibody dilution: 1/250 | Center for Therapeutic Antibody Development at Icahn School of Medicine at Mount Sinai | NP-1C7C7 |
| Anti-cytokeratin 5 AF594 (rabbit polyclonal) antibody dilution: 1/250 | Novus | Cat#NBP2-61931AF594; RRID: AB_2933967 |
| Anti-pan-cytokeratin (clone AE-1/AE-4, mouse IgG1) antibody dilution: 1/300 | BioLegend | Cat#914204; RRID: AB_2616960 |
| Anti-aSMA (clone 1A4, mouse IgG2a) antibody dilution: 1/200 | Abcam | Cat#Ab7817; RRID: AB_262054 |
| Anti-fibronectin (rabbit polyclonal) antibody dilution: 1/400 | Abcam | Cat#Ab32419; RRID: AB_732379 |
| Anti-mouse IgG1 AF488 antibody dilution: 1/2,000 | Thermo Fisher Scientific | Cat#A21121; RRID: AB_2535764 |
| Anti-mouse IgG2a AF647 antibody dilution: 1/2,000 | Thermo Fisher Scientific | Cat#A21241; RRID: AB_2535810 |
| Anti-rabbit IgG AF568 antibody dilution: 1/2,000 | Thermo Fisher Scientific | Cat#A11011; RRID: AB_143157 |
| Anti-mouse IgG2b AF555 antibody dilution: 1/2,000 | Thermo Fisher Scientific | Cat#A-21147; RRID: AB_2535783 |
| Anti-rabbit IgG AF555 antibody dilution: 1/200 | BioLegend | Cat#406412; RRID: AB_2563181 |
| Anti-rat IgG AF488 antibody dilution: 1/2,000 | Thermo Fisher Scientific | Cat#A-11006; RRID: AB_2534074 |
| Anti-NP (SARS-CoV-2; polyclonal) antibody dilution: 1/2,000 | Novus | Cat#NB100-56576A; RRID: AB_838838 |
| Anti-spike (SARS-CoV-2; polyclonal) antibody dilution: 1/50 | Novus | Cat#NBP2-24808AF647; RRID: AB_2933968 |
| Anti-cytokeratin 5 (clone EP1601Y) antibody dilution: 1/60 | Abcam | Cat#ab52635; RRID: AB_869890 |
| Anti-mouse IgG HRP antibody dilution: 1/5,000 | ProteinSimple | Cat# 042-205; RRID: AB_2860576 |
| 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: NDRI | Project: RPAK1 01 |
| Chemicals, peptides, and recombinant proteins | ||
| Advanced DMEM/F12 | Thermo Fisher Scientific | Cat#12634-028 |
| MEM media 10× | Thermo Fisher Scientific | Cat#11430030 |
| GlutaMAX supplement | Thermo Fisher Scientific | Cat#35050-061 |
| Fetal bovine serum | Thermo Fisher Scientific | Cat#50-753-2978 |
| Penicillin/streptomycin (PS) | Thermo Fisher Scientific | Cat#150-70-063 |
| Sodium bicarbonate 7.5% solution | Thermo Fisher Scientific | Cat#25080094 |
| HEPES (1 M) | Thermo Fisher Scientific | Cat#15-630-080 |
| Red blood cell lysis buffer | Roche | Cat#11814389001 |
| 1× PBS | Thermo Fisher Scientific | Cat#70011-044 |
| Cultrex growth factor reduced BME type 2 | Trevigen (R&D Systems) | Cat#3533-010-02 |
| Primocin | InvivoGen | Cat#Ant-pm-1 |
| Nicotinamide | Sigma | Cat#N0636 |
| N-acetylcysteine | Sigma | Cat#A9165 |
| B-27 supplement | Gibco | Cat#1750444 |
| SB202190 | Sigma | Cat#S7067 |
| A83-01 | Tocris | Cat#2939 |
| Noggin | PeproTech | Cat#120-10C |
| FGF 10 | PeproTech | Cat#100-26 |
| FGF 7 | PeproTech | Cat#100-19 |
| R-spondin 1 | PeproTech | Cat#120-38 |
| Y-27632 | AbMole | Cat#M1817 |
| Collagen I rat protein | Thermo Fisher Scientific | Cat#A1048301 |
| PneumaCult-Ex plus medium | STEMCELL | Cat#05040 |
| PneumaCult-ALI medium | STEMCELL | Cat#05001 |
| Hydrocortisone | STEMCELL | Cat#07926 |
| Heparin solution | STEMCELL | Cat#07980 |
| DNase I | Sigma | Cat#D4513 |
| Dispase I | Sigma | Cat#4942086001 |
| Collagenase I | Sigma | Cat#9C9407 |
| Paraformaldehyde 16% | Thermo Fisher Scientific | Cat#28906 |
| Triton X-100 | Thermo Fisher Scientific | Cat#HFH10 |
| Phalloidin ATTO647N | Sigma | Cat#65906 |
| Fluromount-G | Thermo Fisher Scientific | Cat#00-4958-02 |
| DAPI | Thermo Fisher Scientific | 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; for immunofluorescence, IF) | Jackson ImmunoResearch | Cat#001-000-161 |
| BSA (cell culture grade) | Sigma | Cat#A9418 |
| Dimethyl sulfoxide (DMSO) | Sigma | Cat#67-68-5 |
| TrypLE express enzyme | Thermo Fisher Scientific | Cat#12605010 |
| Trypsin-EDTA (0.05%) phenol red | Thermo Fisher Scientific | 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 |
| Oxoid purified agar | Thermo Fisher Scientific | Cat#LP0028 |
| DEAE-dextran | Thermo Fisher Scientific | Cat#J63781.14 |
| TPCK/trypsin | Thermo Fisher Scientific | Cat#20233 |
| TrueBlue peroxidase substrate | SeraCare | Cat#5510-0030 |
| 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 | Omega 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 | Cellosaurus R Matsuyama et al.10 |
Cat#JCRB1819; RRID: CVCL_YQ49 |
| African green monkey (Chlorocebus sabaeus): VeroE6 | ATCC | ATCC CRL-1586, clone E6; RRID: CVCL_0574 |
| Software and algorithms | ||
| Imaris 9.4 | Bitplane | https://imaris.oxinst.com |
| ImageJ | ImageJ | https://imagej.nih.gov/ij/ |
| 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 |
| ComplexHeatmap package (v2.12.1) | R package | https://jokergoo.github.io/ComplexHeatmap/ |
| RSEM v1.3.3 | Li and Dewey11 | https://github.com/deweylab/RSEM/releases/tag/v1.3.3 |
| Bowtie | Langmead et al.12 | http://bowtie-bio.sourceforge.net/index.shtml |
| FastQC | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ | N/A |
| MultiQC | Ewels et al.13 | N/A |
| BBDuk tool | BBMap download | SourceForge.net | https://sourceforge.net/projects/bbmap/ |
| DESeq2 | R package Love et al.14 |
N/A |
| SVAseq | R package | https://doi.org/10.1093/nar/gku864 |
| Reference manager | Mendeley | https://www.mendeley.com/search/ |
| Other | ||
| Greiner CELLSTAR multiwell culture plates (P24-well) | Sigma | Cat#M9312 |
| Corning Transwell polyester membrane cell culture inserts (P24-well, 0.4 μm) | Sigma | Cat#3470 |
| Corning sterile cell strainers (100 μm) | Fisher Scientific | Cat#431752 |
| Petri dishes 100 × 15 mm | Thermo Fisher Scientific | Cat#150350 |
| Petri dishes 60 × 15 mm | Thermo Fisher Scientific | Cat#174888 |
| 50 mL tubes | Fisher Scientific | Cat#339652 |
| 2 mL cryovial tubes | Fisher Scientific | Cat#431386 |
| Tissue-Tek OCT compound | Thermo Fisher Scientific | Cat#4583 |
| Tissue-Tek cryomold | VWR | Cat#4566 |
| Slides | Denville Scientific | Cat#M1021 |
| Cover glass | Thermo Scientific | Cat#152450 |
| Optimized freezing container | Thermo Fisher Scientific | Cat#5100-0001 |
| MACSmix tube rotator | Miltenyi Biotec | Cat#130-090-753 |
| EVOM2 ohm meter | WPI | Cat#EVOM2 |
| Piston from insulin syringe | BD Biosciences | Cat#324921 |
| Membrane filter, 0.22 μm pore size | Sigma | Cat#GSWP04700 |
| Beakers (1,000 mL) | VWR | Cat#13912-284 |
| Pyrex container | Cole-Parmer | Cat#3175-10 |
| Autoclaving foil | VWR | Cat#47734-154 |
| Saran wrap | VWR | Cat#46610-056 |
| Parafilm | VWR | Cat#52858-076 |
| Surgical blue wrap | VWR | Cat#56222-053 |
| Scalpel | VWR | Cat#76457-484 |
| Surgical forceps | VWR | Cat#10806-206 |
| Fine-point forceps | VWR | Cat#470005-440 |
| Surgical scissors | VWR | Cat#76457-366 |
| Pipet-Lite LTS pipette L-1000XLS+ | Rainin | Cat#17014382 |
| Pipettes (tips 1 mL) | Mettler Toledo | Cat#30389217 |
| Electric pipette controller Eppendorf Easypet 3 | Eppendorf | Cat#2231000955 |
| Serological pipettes (10 mL) | Thermo Fisher Scientific | Cat#170356N |
| Serological pipettes (25 mL) | Thermo Fisher Scientific | Cat#170357N |
| Schematic and graphical abstract images | BioRender | https://www.biorender.com |
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