| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Phospho-p38 MAPK (Thr180/Tyr182) | Cell Signaling | Cat#9211S |
| ɑ-Rabbit IgG HRP Conjugate | Biorad | Cat#1706515 |
| ɑ-Mouse IgG HRP Conjugate | Biorad | Cat#1706516 |
| SARS-CoV-2 N (recombinant mouse monoclonal) | Donated from the laboratory of Thomas Moran (Mount Sinai) | N/A |
| GAPDH | Cell Signaling | Cat#2118S |
| Phospho-MAPKAPK2 (T334) | Cell Signaling | Cat#3007T |
| Phospho-CREB/ATF-1 (S133) | Cell Signaling | Cat#9198S |
| CK2α | Abcam | Cat#ab70774 |
| SARS-CoV membrane (M) | Rockland | Cat#100-401-A55 |
| SARS-CoV nucleocapsid (N) | Rockland | Cat#200-401-A50 |
| AF568-labeled goat-anti-rabbit | InvitrogenCat# | Cat#A11011 |
| AF647-labeled goat-anti-mouse | Invitrogen | Cat#A21235 |
| AF488-labeled Phalloidin | Hypermol | Cat#8813-01 |
| viral NP protein anti-sera | produced in the Garcia-Sastre lab | N/A |
| Bacterial and Virus Strains | ||
| SARS-CoV-2, isolate BetaCoV/France/IDF0372/2020 | European Virus Archive goes Global (EVAg) | IDF0372/2020 |
| SARS-CoV-2, isolate USA-WA1/2020 | BEI Resources | Cat#NR-52281 |
| SARS-CoV-2, Isolate Muc-IMB-1/2020 | Bundeswehr Institute of Microbiology, Munich, Germany | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| cOmplete protease inhibitor cocktail tablets mini, EDTA-free | Roche | Cat#11846170001 |
| PhosStop phosphatase inhibitor cocktail tablets | Roche | Cat#4906837001 |
| Sep-Pak C18 cartridge | Waters | Cat#WAT054955 |
| Sequencing-grade modified trypsin | Promega | Cat#V5111 |
| Fetal bovine serum (FBS) | Thermo Fisher Scientific | Cat#10082 |
| DMEM | Thermo Fisher Scientific | Cat#MT10013CV |
| Water, HPLC grade | Sigma-Aldrich | Cat#270733-4 L; CAS#7732-18-5 |
| Ni-NTA Superflow beads | QIAGEN | Cat#30210 |
| Igepal | Sigma-Aldrich | Cat#I3021; CAS#9002-93-1 |
| Minimal Essential Media (MEM) | Corning | Cat#10-009-CV |
| Opti-MEM | Thermo Fisher Scientific | Cat#31985062 |
| Paraformaldehyde, 4% solution in PBS (PFA) | Thermo Scientific | Cat#MFCD00133991 |
| Formalin | Fisher Scientific | Cat#SF100-20; CAS#50-00-0, 67-56-1, 7558-79-4, 10049-21-5, 7732-18-5 |
| 4′,6-diamidino-2-phenylindole (DAPI) | Thermo Scientific | Cat#62247 |
| ReprosilPur 1.9 μm particles | ESI SOURCE SOLUTIONS | Cat#R119 |
| Crystal Violet Solution | Sigma Aldrich | Cat#HT90132-1L |
| Thermanox coverslips | Ted Pella | Cat#26028 |
| Silicon Chips | Ted Pella | Cat#16007 |
| Aluminum specimen mounts | Ted Pella | Cat#16111 |
| Double-sided carbon tape | Ted Pella | Cat#16084-1 |
| Karnovsky’s EM fixative | Electron Microscopy Sciences | Cat#15720 |
| Sodium Cacodylate | Sigma | Cat#C4945-10G; CAS#6131-99-3 |
| Osmium Tetroxide | Electron Microscopy Sciences | Cat#19190; CAS#20816-12-0 |
| Potassium Ferrocyanide | Sigma | Cat#P-3289; CAS#14459-95-1 |
| Uranyl Acetate | Ted Pella | Cat#19481; CAS#6159-44-0 |
| Spurr’s resin | Ted Pella | Cat#18300-4221 |
| Iridium target | Electron Microscopy Sciences | Cat#3431 |
| PolyJet | SignaGen | Cat#SL100688 |
| SuperScript IV Reverse Transcriptase | Invitrogen | Cat#18090010 |
| ARRY-371797 (ARRY-797) | MedKoo Biosciences | Cat#555466; CAS#1036404-17-7 |
| Dilmapimod (SB-681323) | MedChemExpress | Cat#HY-10404; CAS#444606-18-2 |
| Doramapimod (BIRB-796) | SelleckChem | Cat#S1574; CAS#285983-48-4 |
| Losmapimod | SelleckChem | Cat#S7215; CAS#585543-15-3 |
| MAPK13-IN-1 | MedChemExpress | Cat#HY-18850; CAS#229002-10-2 |
| Neflamapimod (VX-745) | SelleckChem | Cat#S1458; CAS#209410-46-8 |
| P38 MAPK Inhibitor (4) | Cayman Chemical | Cat#22219; CAS#1638-41-1 |
| PF-3644022 | Tocris Bioscience | Cat#4483; CAS#142557-61-7 |
| PH-797804 | SelleckChem | Cat#S2726; CAS#586379-66-0 |
| Ralimetinib (LY2228820) | SelleckChem | Cat#S1494; CAS#862507-23-1 |
| SB203580 | SelleckChem | Cat#S1076; CAS#152121-47-6 |
| TAK-715 | SelleckChem | Cat#S2928; CAS#303162-79-0 |
| Talmapimod (SCIO-469) | MedChemExpress | Cat#HY-10406; CAS#309913-83-5 |
| VX-702 | SelleckChem | Cat#S6005; CAS#745833-23-2 |
| 4EGI-1 | SelleckChem | Cat#S7369; CAS#315706-13-9 |
| A-484954 | Tocris Bioscience | Cat#4279; CAS#1276121-88-0 |
| Abemaciclib mesylate | SelleckChem | Cat#S7158; CAS#1231930-82-7 |
| Alisertib | SelleckChem | Cat#S1133; CAS#1028486-01-2 |
| Apilimod | SelleckChem | Cat#S6414; CAS#541550-19-0 |
| AT-13148 | SelleckChem | Cat#S7563; CAS#1056901-62-2 |
| AZD-1208 | SelleckChem | Cat#S7104; CAS#1204144-28-4 |
| AZD-5363 (Capivasertib) | SelleckChem | Cat#S8019; CAS#1143532-39-1 |
| AZD-7648 | SelleckChem | Cat#S8843; CAS#2230820-11-6 |
| Bafetinib | SelleckChem | Cat#S1369; CAS#859212-16-1 |
| BMS-582949 | SelleckChem | Cat#S8124; CAS#623152-17-0 |
| Bortezomib (PS-341) | SelleckChem | Cat#S1013; CAS#179324-69-7 |
| CHIR-98014 | SelleckChem | Cat#S2745; CAS#252935-94-7 |
| Dabrafenib (GSK2118436) | SelleckChem | Cat#S2807; CAS#1195765-45-7 |
| Dasatinib | SelleckChem | Cat#S1021; CAS#302962-49-8 |
| Dinaciclib | SelleckChem | Cat#S2768; CAS#779353-01-4 |
| Dorsomorphin 2HCl | SelleckChem | Cat#S7306; CAS#1219168-18-9 |
| EHT 1864 2HCl | SelleckChem | Cat#S7482; CAS#754240-09-0 |
| Enzastaurin | SelleckChem | Cat#S1055; CAS#170364-57-5 |
| Fludarabine | SelleckChem | Cat#S1491; CAS#S1491 |
| Fosbretabulin (Combretastatin A4 Phosphate (CA4P)) Disodium | SelleckChem | Cat#S7204; CAS#168555-66-6 |
| Ganetespib | SelleckChem | Cat#S1159; CAS#888216-25-9 |
| Gilteritinib | SelleckChem | Cat#S7754; CAS#1254053-43-4 |
| Idarubicin HCl | SelleckChem | Cat#S1228; CAS#57852-57-0 |
| Ipatasertib | SelleckChem | Cat#S2808; CAS#1001264-89-6 |
| Ispinesib (SB-715992) | SelleckChem | Cat#S1452; CAS#336113-53-2 |
| Ixazomib (MLN2238) | SelleckChem | Cat#S2180; CAS#1072833-77-2 |
| K-252a | Cayman Chemical | Cat#11338; CAS#99533-80-9 |
| KenPaullone | SelleckChem | Cat#S7917; CAS#142273-20-9 |
| KW-2449 | SelleckChem | Cat#S2158; CAS#1000669-72-6 |
| LJI308 | SelleckChem | Cat#S7871; CAS#1627709-94-7 |
| LMK-235 | SelleckChem | Cat#S7569; CAS#1418033-25-6 |
| LY2584702 Tosylate | SelleckChem | Cat#S7704; CAS#1082949-68-5 |
| MBQ-167 | SelleckChem | Cat#S8749; CAS#2097938-73-1 |
| Mdivi-1 | SelleckChem | Cat#S7162; CAS#338967-87-6 |
| Midostaurin | SelleckChem | Cat#S8064; CAS#120685-11-2 |
| MK-2206 2HCl | SelleckChem | Cat#S1078; CAS#1032350-13-2 |
| ML141 | SelleckChem | Cat#S7686; CAS#71203-35-5 |
| NSC319276 | SelleckChem | Cat#S7149; CAS#71555-25-4 |
| NVP-BEP800 | SelleckChem | Cat#S1498; CAS#847559-80-2 |
| Palbociclib (PD-0332991) HCl | SelleckChem | Cat#S1116; CAS#827022-32-2 |
| PF-03814735 | SelleckChem | Cat#S2725; CAS#942487-16-3 |
| PF-3758309 | SelleckChem | Cat#S7094; CAS#898044-15-0 |
| PHA-793887 | SelleckChem | Cat#S1487; CAS#718630-59-2 |
| Pictilisib | SelleckChem | Cat#S1065; CAS#957054-30-7 |
| PKR Inhibitor | Cayman Chemical | Cat#15323; CAS#608512-97-6 |
| QNZ (EVP4593) | SelleckChem | Cat#S4902; CAS#545380-34-5 |
| R-406 | SelleckChem | Cat#S2194; CAS#841290-81-1 |
| R-547 | SelleckChem | Cat#S2688; CAS#741713-40-6 |
| Rapamycin | SelleckChem | Cat#S1039; CAS#53123-88-9 |
| Ravoxertinib | SelleckChem | Cat#S7554; CAS#1453848-26-4 |
| Remdesivir | BioVision | Cat#B2997; CAS#1809249-37-3 |
| Ripasudil (K-115) hydrochloride dihydrate | SelleckChem | Cat#S7995; CAS#887375-67-9 |
| Romidepsin (FK228, Depsipeptide) | SelleckChem | Cat#S3020; CAS#128517-07-7 |
| Ruboxistaurin HCl(LY333531) | SelleckChem | Cat#S7663; CAS#169939-93-9 |
| Sapanisertib | SelleckChem | Cat#S2811; CAS#1224844-38-5 |
| SAR-407899 | Cayman Chemical | Cat#21717; CAS#923359-38-0 |
| SB743921 HCl | SelleckChem | Cat#S2182; CAS#940929-33-9 |
| SGI-1776 free base | SelleckChem | Cat#S2198; CAS#1025065-69-3 |
| Silmitasertib | SelleckChem | Cat#S2248; CAS#1009820-21-6 |
| Sorafenib Tosylate | SelleckChem | Cat#S1040; CAS#475207-59-1 |
| Sotrastaurin | SelleckChem | Cat#S2791; CAS#425637-18-9 |
| Stattic | SelleckChem | Cat#S7024; CAS#19983-44-9 |
| Staurosporine | SelleckChem | Cat#S1421; CAS#62996-74-1 |
| Tanzisertib | SelleckChem | Cat#S8490; CAS#899805-25-5(freebase) |
| Tasquinimod | SelleckChem | Cat#S7617; CAS#254964-60-8 |
| THZ1 2HCl | SelleckChem | Cat#S7549; CAS#1604810-83-4(freebase) |
| Tpl2 Kinase Inhibitor 1 | Cayman Chemical | Cat#19710; CAS#871307-18-5 |
| U73122 | SelleckChem | Cat#S8011; CAS#112648-68-7 |
| Volasertib | SelleckChem | Cat#S2235; CAS#755038-65-4 |
| XL413 (BMS-863233) | SelleckChem | Cat#S7547; CAS#1169562-71-3 |
| Y-39983 HCl | SelleckChem | Cat#S7935; CAS#173897-44-4 |
| CCL2/MCP-1, Capture Antibody | R&D Systems | Cat#MAB679 |
| CCL5/RANTES, Capture Antibody | R&D Systems | Cat#MAB678 |
| CCL11/Eotaxin, Capture Antibody | R&D Systems | Cat#MAB320 |
| GM-CSF, Capture Antibody | R&D Systems | Cat#MAB615 |
| IL-1RA, Capture Antibody | Peprotech | Cat#500-P209 |
| CCL13/MCP-4, Capture Antibody | R&D Systems | Cat#MAB327 |
| IL-4, Capture Antibody | R&D Systems | Cat#MAB604 |
| IL-10, Capture Antibody | Peprotech | Cat#500-P20 |
| IL-15, Capture Antibody | R&D Systems | Cat#MAB647 |
| IL-1beta, Capture Antibody | R&D Systems | Cat#MAB601 |
| CCL8/MCP-2, Capture Antibody | Peprotech | Cat#500-P35 |
| CXCL9/MIG, Capture Antibody | Peprotech | Cat#500-P50 |
| CCL3/MIP-1alpha, Capture Antibody | R&D Systems | Cat#MAB670 |
| CXCL2/GRO-Beta, Capture Antibody | Peprotech | Cat#500-P104 |
| TGF-Beta1, Capture Antibody | R&D Systems | Cat#MAB240 |
| CXCL16, Capture Antibody | Peprotech | Cat#500-P200 |
| CXCL8/IL-8, Capture Antibody | R&D Systems | Cat#MAB208 |
| MMP-9, Capture Antibody | R&D Systems | Cat#MAB936 |
| CXCL1/GRO-alpha, Capture Antibody | Peprotech | Cat#500-P92 |
| IL-7, Capture Antibody | R&D Systems | Cat#MAB207 |
| CCL4/MIP-1beta, Capture Antibody | R&D Systems | Cat#MAB271 |
| IL-1alpha, Capture Antibody | R&D Systems | Cat#MAB200 |
| IL-12 (p70), Capture Antibody | Peprotech | Cat#500-P154G |
| IL-16, Capture Antibody | R&D Systems | Cat#MAB316 |
| CCL20/MIP-3a, Capture Antibody | R&D Systems | Cat#MAB360 |
| TNF-alpha, Capture Antibody | R&D Systems | Cat#MAB610 |
| Trappin-2/Elafin, Capture Antibody | R&D Systems | Cat#AF1747 |
| IL-17A, Capture Antibody | R&D Systems | Cat#MAB317 |
| CXCL10/IP-10, Capture Antibody | R&D Systems | Cat#MAB266 |
| S100A8, Capture Antibody | R&D Systems | Cat#DS8900 |
| IL-22, Capture Antibody | Peprotech | Cat#500-P211 |
| CXCL5/ENA-78, Capture Antibody | R&D Systems | Cat#MAB654 |
| IL-6, Capture Antibody | R&D Systems | Cat#MAB206 |
| CCL7/MCP-3, Capture Antibody | R&D Systems | Cat#MAB282 |
| CCL2/MCP-1, Protein std | R&D Systems | Cat#279-MC |
| CCL5/RANTES, Protein std | R&D Systems | Cat#278-RN |
| CCL11/Eotaxin, Protein std | Peprotech | Cat#300-21 |
| GM-CSF, Protein std | R&D Systems | Cat#215-GM |
| IL-1RA, Protein std | Peprotech | Cat#200-01RA |
| CCL13/MCP-4, Protein std | R&D Systems | Cat#327-P4 |
| IL-4, Protein std | R&D Systems | Cat#204-IL |
| IL-10, Protein std | Peprotech | Cat#200-10 |
| IL-15, Protein std | R&D Systems | Cat#247-ILB |
| IL-1beta, Protein std | R&D Systems | Cat#201-LB |
| CCL8/MCP-2, Protein std | Peprotech | Cat#300-15 |
| CXCL9/MIG, Protein std | R&D Systems | Cat#392-MG |
| CCL3/MIP-1alpha, Protein std | R&D Systems | Cat#270-LD |
| CXCL2/GRO-Beta, Protein std | Peprotech | Cat#300-39 |
| TGF-Beta1, Protein std | Peprotech | Cat#100-21 |
| CXCL16, Protein std | Peprotech | Cat#300-55 |
| CXCL8/IL-8, Protein std | R&D Systems | Cat#208-IL |
| MMP-9, Protein std | R&D Systems | Cat#911-MP |
| CXCL1/GRO-alpha, Protein std | Peprotech | Cat#300-11 |
| IL-7, Protein std | R&D Systems | Cat#207-IL |
| CCL4/MIP-1beta, Protein std | R&D Systems | Cat#271-BME |
| IL-1alpha, Protein std | Peprotech | Cat#200-01A |
| IL-12(p70), Protein std | R&D Systems | Cat#219-IL |
| IL-16, Protein std | Peprotech | Cat#200-16 |
| CCL20/MIP-3a, Protein std | Peprotech | Cat#300-29A |
| TNF-alpha, Protein std | R&D Systems | Cat#210-TA |
| Trappin-2/Elafin, Protein std | R&D Systems | Cat#1747-PI |
| IL-17A, Protein std | Peprotech | Cat#200-17 |
| CXCL10/IP-10, Protein std | R&D Systems | Cat#266-IP |
| S100A8, Protein std | R&D Systems | Cat#DS8900 |
| IL-22, Protein std | Peprotech | Cat#200-22 |
| CXCL5/ENA-78, Protein std | R&D Systems | Cat#254-XB |
| IL-6, Protein std | R&D Systems | Cat#206-IL |
| CCL7/MCP-3, Protein std | R&D Systems | Cat#282-P3 |
| CCL2/MCP-1, Detection Antibody | R&D Systems | Cat#BAF279 |
| CCL5/RANTES, Detection Antibody | R&D Systems | Cat#BAF278 |
| CCL11/Eotaxin, Detection Antibody | R&D Systems | Cat#BAF320 |
| GM-CSF, Detection Antibody | R&D Systems | Cat#BAM 215 |
| IL-1RA, Detection Antibody | Peprotech | Cat#500-P209BT |
| CCL13/MCP-4, Detection Antibody | R&D Systems | Cat#BAF327 |
| IL-4, Detection Antibody | R&D Systems | Cat#BAF204 |
| IL-10, Detection Antibody | Peprotech | Cat#500-P20BT |
| IL-15, Detection Antibody | R&D Systems | Cat#BAM 247 |
| IL-1beta, Detection Antibody | R&D Systems | Cat#BAF201 |
| CCL8/MCP-2, Detection Antibody | Peprotech | Cat#500-P35BT |
| CXCL9/MIG, Detection Antibody | Peprotech | Cat#500-P50BT |
| CCL3/MIP-1alpha, Detection Antibody | R&D Systems | Cat#BAF270 |
| CXCL2/GRO-Beta, Detection Antibody | Peprotech | Cat#500P104BT |
| TGF-Beta1, Detection Antibody | R&D Systems | Cat#BAM 2462 |
| CXCL16, Detection Antibody | Peprotech | Cat#500-P200BT |
| CXCL8/IL-8, Detection Antibody | R&D Systems | Cat#BAF208 |
| MMP-9, Detection Antibody | R&D Systems | Cat#BAF911 |
| CXCL1/GRO-alpha, Detection Antibody | Peprotech | Cat#500P92BT |
| IL-7, Detection Antibody | R&D Systems | Cat#BAF207 |
| CCL4/MIP-1beta, Detection Antibody | R&D Systems | Cat#BAF271 |
| IL-1alpha, Detection Antibody | R&D Systems | Cat#BAF200 |
| IL-12(p70), Detection Antibody | Peprotech | Cat#500-P154GBT |
| IL-16, Detection Antibody | R&D Systems | Cat#BAF316 |
| CCL20/MIP-3a, Detection Antibody | R&D Systems | Cat#BAF360 |
| TNF-alpha, Detection Antibody | R&D Systems | Cat#BAF210 |
| Trappin-2/Elafin, Detection Antibody | R&D Systems | Cat#BAF1747 |
| IL-17A, Detection Antibody | R&D Systems | Cat#BAF317 |
| CXCL10/IP-10, Detection Antibody | Peprotech | Cat#500-P93BT |
| S100A8, Detection Antibody | R&D Systems | Cat#DS8900 |
| IL-22, Detection Antibody | Peprotech | Cat#500-P211BT |
| CXCL5/ENA-78, Detection Antibody | R&D Systems | Cat#BAF254 |
| IL-6, Detection Antibody | R&D Systems | Cat#BAF206 |
| CCL7/MCP-3, Detection Antibody | R&D Systems | Cat#BAF282 |
| Critical Commercial Assays | ||
| MTT assay | Roche | Cat#11465007001 |
| Luna Universal One-Step RT-qPCR Kit | New England Biolabs | Cat#E3005L |
| CellTiter-Glo Luminescent Cell Viability Assay | Promega | Cat#G7570 |
| Direct-zol RNA Miniprep Plus kit | Zymo Research | Cat#R2072 |
| KAPA SYBR FAST qPCR Master Mix | Roche | Cat#07959389001 |
| Bio-Rad II Protein Assay Kit | Bio-Rad | Cat#5000002 |
| Deposited Data | ||
| Phosphoproteomics data of SARS-CoV-2 infected Vero E6 cells | This paper | PRIDE Project ID: PXD019113 |
| Supplemental Tables in Mendeley Data | This paper | https://dx.doi.org/10.17632/dpkbh2g9hy.1 |
| CORUM v3.0 | Giurgiu et al., 2019 | http://mips.helmholtz-muenchen.de/corum/ |
| RNA-seq dataset for transcription factor activities | Blanco-Melo et al., 2020 | GSE147507 |
| Phosphoproteomics datasets of biological conditions | Ochoa et al., 2016 | https://www.embopress.org/doi/full/10.15252/msb.20167295 |
| Functional scores for phosphorylation sites | Ochoa et al., 2020 | https://idp.nature.com/authorize?response_type=cookie&client_id=grover&redirect_uri=https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41587-019-0344-3 |
| Gene identifier mapping database from BioMart | Ensembl | http://uswest.ensembl.org/biomart/martview/5ccd994c794265409f21c6194730ce5b |
| Molecular Signatures Database for gene set enrichment analysis | Subramanian et al., 2005 | https://www.gsea-msigdb.org/gsea/msigdb/index.jsp |
| Kinase-substrate relationships | Bachman et al., 2019 | https://www.biorxiv.org/content/10.1101/822668v3.full |
| Chlorocebus proteome sequences for peptide searches | Uniprot | https://www.uniprot.org/proteomes/UP000029965 |
| Sars-CoV-2 genomic sequences (hCoV-19/France/IDF0372/2020) | GISAID | Accession number EPI_ISL_406596 |
| Experimental Models: Cell Lines | ||
| ACE2-A549 human lung carcinoma | Donated from the laboratory of Brad Rosenberg | N/A |
| Caco-2 | ATCC | Cat#HTB-37 |
| VERO C1008 [Vero 76, clone E6, Vero E6] (Vero E6) | ATCC | Cat#CRL-1586 |
| HEK293T/17 cells | ATCC | Cat#CRL-11268 |
| Oligonucleotides | ||
| ON-TARGETplus Human MAPK12 (6300) siRNA - SMARTpool, 5 nmol | Horizon Discovery/Dharmacon | Cat#L-003590-00-0005 |
| ON-TARGETplus Human MAPK13 (5603) siRNA - SMARTpool, 5 nmol | Horizon Discovery/Dharmacon | Cat#L-003591-00-0005 |
| ON-TARGETplus Human MAP2K3 (5606) siRNA - SMARTpool, 5 nmol | Horizon Discovery/Dharmacon | Cat#L-003509-00-0005 |
| ON-TARGETplus Human ACE2 (59272) siRNA - SMARTpool | Horizon Discovery/Dharmacon | Cat#L-005755-00-0005 |
| N gene region (reverse) 5′-CGAAGGTGTGACTTCCATG-3′ | Eurofins | N/A |
| N gene region (forward) 5′-TAATCAGACAAGGAACTGATTA-3′ |
Eurofins | N/A |
| Recombinant DNA | ||
| pLVX-TetOne-Puro empty vector | Takara | Cat#631847 |
| pLVX-TetOne-Puro-SARS-CoV-2-N-2xStrep | This paper | N/A |
| pMD2.G, Addgene | Gift from Didier Trono | Addgene Plasmid #12259 |
| Gag-Pol-Tat-Rev packaging construct | Gift from Judd Hultquist | pJH045 |
| Software and Algorithms | ||
| artMS | Bioconductor | https://www.bioconductor.org/packages/release/bioc/html/artMS.html |
| MSstats | Bioconductor | https://www.bioconductor.org/packages/release/bioc/html/artMS.html |
| The R Project for Statistical Computing | R Core Team, 2019 | http://www.r-project.org/index.html |
| Spectronaut | Biognosys | https://biognosys.com/shop/spectronaut |
| ZEN (Blue edition) | Carl Zeiss Microscopy | https://www.zeiss.com/zen |
| SPPIDER v2 | Porollo and Meller, 2007 | http://sppider.cchmc.org/ |
| DoRothEA | Garcia-Alonso et al., 2019 | https://saezlab.github.io/dorothea/ |
| VIPER | Alvarez et al., 2016 | https://www.bioconductor.org/packages/release/bioc/html/viper.html |
| Biostrings | Bioconductor | https://bioconductor.org/packages/release/bioc/html/Biostrings.html |
| clusterProfiler | Bioconductor | https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html |
| DESeq2 package | Love et al., 2014 | http://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Imaris 64x 9.5.1 | Oxford Instruments | https://imaris.oxinst.com/ |
| MetaMorph (Version 7.8) | Molecular Devices | https://www.moleculardevices.com/ |
| Other | ||
| Orbitrap Exploris 480 MS with internal calibration option | Thermo Fisher Scientific | Cat#BRE725533 |
| ZEISS LSM 800 Confocal Laser Scanning Microscope | Carl Zeiss Microscopy | Model#ZEISS LSM 800 |
| QuantStudio 6 Real-Time PCR System | Applied Biosystems | Cat#4485697 |
| FACSymphony | BD Life Sciences | N/A |
| Infinity 2000 Plate Reader | Tecan | N/A |
| Luminex MAGPIX platform | Luminex Corp | N/A |
| LightCycler 480 Instrument II | Roche | N/A |
| Bal-Tec Drier | Balzers, Liechtenstein | Cat#CPD 030 |
| Quorum sputter coater | Electron Microscopy Sciences, Hatfield, PA | Cat#EMS300T D |
| Hitachi field emission scanning electron microscope | Hitachi, Tokyo, Japan | Model#SU-8000 |
| Leica UC7 ultramicrotome | Leica Microsystems | N/A |
| FEI BT Tecnai transmission electron microscope | Thermofisher/FEI | N/A |
| Gatan Rio camera | Gatan | N/A |
| Celigo imaging cytometer | Nexcelcom | N/A |
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