PMC:7321036 / 58272-75349 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7321036","sourcedb":"PMC","sourceid":"7321036","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7321036","text":"Key Resources Table\nREAGENT or RESOURCE SOURCE IDENTIFIER\nAntibodies\nPhospho-p38 MAPK (Thr180/Tyr182) Cell Signaling Cat#9211S\nɑ-Rabbit IgG HRP Conjugate Biorad Cat#1706515\nɑ-Mouse IgG HRP Conjugate Biorad Cat#1706516\nSARS-CoV-2 N (recombinant mouse monoclonal) Donated from the laboratory of Thomas Moran (Mount Sinai) N/A\nGAPDH Cell Signaling Cat#2118S\nPhospho-MAPKAPK2 (T334) Cell Signaling Cat#3007T\nPhospho-CREB/ATF-1 (S133) Cell Signaling Cat#9198S\nCK2α Abcam Cat#ab70774\nSARS-CoV membrane (M) Rockland Cat#100-401-A55\nSARS-CoV nucleocapsid (N) Rockland Cat#200-401-A50\nAF568-labeled goat-anti-rabbit InvitrogenCat# Cat#A11011\nAF647-labeled goat-anti-mouse Invitrogen Cat#A21235\nAF488-labeled Phalloidin Hypermol Cat#8813-01\nviral NP protein anti-sera produced in the Garcia-Sastre lab N/A\nBacterial and Virus Strains\nSARS-CoV-2, isolate BetaCoV/France/IDF0372/2020 European Virus Archive goes Global (EVAg) IDF0372/2020\nSARS-CoV-2, isolate USA-WA1/2020 BEI Resources Cat#NR-52281\nSARS-CoV-2, Isolate Muc-IMB-1/2020 Bundeswehr Institute of Microbiology, Munich, Germany N/A\nChemicals, Peptides, and Recombinant Proteins\ncOmplete protease inhibitor cocktail tablets mini, EDTA-free Roche Cat#11846170001\nPhosStop phosphatase inhibitor cocktail tablets Roche Cat#4906837001\nSep-Pak C18 cartridge Waters Cat#WAT054955\nSequencing-grade modified trypsin Promega Cat#V5111\nFetal bovine serum (FBS) Thermo Fisher Scientific Cat#10082\nDMEM Thermo Fisher Scientific Cat#MT10013CV\nWater, HPLC grade Sigma-Aldrich Cat#270733-4 L; CAS#7732-18-5\nNi-NTA Superflow beads QIAGEN Cat#30210\nIgepal Sigma-Aldrich Cat#I3021; CAS#9002-93-1\nMinimal Essential Media (MEM) Corning Cat#10-009-CV\nOpti-MEM Thermo Fisher Scientific Cat#31985062\nParaformaldehyde, 4% solution in PBS (PFA) Thermo Scientific Cat#MFCD00133991\nFormalin Fisher Scientific Cat#SF100-20; CAS#50-00-0, 67-56-1, 7558-79-4, 10049-21-5, 7732-18-5\n4′,6-diamidino-2-phenylindole (DAPI) Thermo Scientific Cat#62247\nReprosilPur 1.9 μm particles ESI SOURCE SOLUTIONS Cat#R119\nCrystal Violet Solution Sigma Aldrich Cat#HT90132-1L\nThermanox coverslips Ted Pella Cat#26028\nSilicon Chips Ted Pella Cat#16007\nAluminum specimen mounts Ted Pella Cat#16111\nDouble-sided carbon tape Ted Pella Cat#16084-1\nKarnovsky’s EM fixative Electron Microscopy Sciences Cat#15720\nSodium Cacodylate Sigma Cat#C4945-10G; CAS#6131-99-3\nOsmium Tetroxide Electron Microscopy Sciences Cat#19190; CAS#20816-12-0\nPotassium Ferrocyanide Sigma Cat#P-3289; CAS#14459-95-1\nUranyl Acetate Ted Pella Cat#19481; CAS#6159-44-0\nSpurr’s resin Ted Pella Cat#18300-4221\nIridium target Electron Microscopy Sciences Cat#3431\nPolyJet SignaGen Cat#SL100688\nSuperScript IV Reverse Transcriptase Invitrogen Cat#18090010\nARRY-371797 (ARRY-797) MedKoo Biosciences Cat#555466; CAS#1036404-17-7\nDilmapimod (SB-681323) MedChemExpress Cat#HY-10404; CAS#444606-18-2\nDoramapimod (BIRB-796) SelleckChem Cat#S1574; CAS#285983-48-4\nLosmapimod SelleckChem Cat#S7215; CAS#585543-15-3\nMAPK13-IN-1 MedChemExpress Cat#HY-18850; CAS#229002-10-2\nNeflamapimod (VX-745) SelleckChem Cat#S1458; CAS#209410-46-8\nP38 MAPK Inhibitor (4) Cayman Chemical Cat#22219; CAS#1638-41-1\nPF-3644022 Tocris Bioscience Cat#4483; CAS#142557-61-7\nPH-797804 SelleckChem Cat#S2726; CAS#586379-66-0\nRalimetinib (LY2228820) SelleckChem Cat#S1494; CAS#862507-23-1\nSB203580 SelleckChem Cat#S1076; CAS#152121-47-6\nTAK-715 SelleckChem Cat#S2928; CAS#303162-79-0\nTalmapimod (SCIO-469) MedChemExpress Cat#HY-10406; CAS#309913-83-5\nVX-702 SelleckChem Cat#S6005; CAS#745833-23-2\n4EGI-1 SelleckChem Cat#S7369; CAS#315706-13-9\nA-484954 Tocris Bioscience Cat#4279; CAS#1276121-88-0\nAbemaciclib mesylate SelleckChem Cat#S7158; CAS#1231930-82-7\nAlisertib SelleckChem Cat#S1133; CAS#1028486-01-2\nApilimod SelleckChem Cat#S6414; CAS#541550-19-0\nAT-13148 SelleckChem Cat#S7563; CAS#1056901-62-2\nAZD-1208 SelleckChem Cat#S7104; CAS#1204144-28-4\nAZD-5363 (Capivasertib) SelleckChem Cat#S8019; CAS#1143532-39-1\nAZD-7648 SelleckChem Cat#S8843; CAS#2230820-11-6\nBafetinib SelleckChem Cat#S1369; CAS#859212-16-1\nBMS-582949 SelleckChem Cat#S8124; CAS#623152-17-0\nBortezomib (PS-341) SelleckChem Cat#S1013; CAS#179324-69-7\nCHIR-98014 SelleckChem Cat#S2745; CAS#252935-94-7\nDabrafenib (GSK2118436) SelleckChem Cat#S2807; CAS#1195765-45-7\nDasatinib SelleckChem Cat#S1021; CAS#302962-49-8\nDinaciclib SelleckChem Cat#S2768; CAS#779353-01-4\nDorsomorphin 2HCl SelleckChem Cat#S7306; CAS#1219168-18-9\nEHT 1864 2HCl SelleckChem Cat#S7482; CAS#754240-09-0\nEnzastaurin SelleckChem Cat#S1055; CAS#170364-57-5\nFludarabine SelleckChem Cat#S1491; CAS#S1491\nFosbretabulin (Combretastatin A4 Phosphate (CA4P)) Disodium SelleckChem Cat#S7204; CAS#168555-66-6\nGanetespib SelleckChem Cat#S1159; CAS#888216-25-9\nGilteritinib SelleckChem Cat#S7754; CAS#1254053-43-4\nIdarubicin HCl SelleckChem Cat#S1228; CAS#57852-57-0\nIpatasertib SelleckChem Cat#S2808; CAS#1001264-89-6\nIspinesib (SB-715992) SelleckChem Cat#S1452; CAS#336113-53-2\nIxazomib (MLN2238) SelleckChem Cat#S2180; CAS#1072833-77-2\nK-252a Cayman Chemical Cat#11338; CAS#99533-80-9\nKenPaullone SelleckChem Cat#S7917; CAS#142273-20-9\nKW-2449 SelleckChem Cat#S2158; CAS#1000669-72-6\nLJI308 SelleckChem Cat#S7871; CAS#1627709-94-7\nLMK-235 SelleckChem Cat#S7569; CAS#1418033-25-6\nLY2584702 Tosylate SelleckChem Cat#S7704; CAS#1082949-68-5\nMBQ-167 SelleckChem Cat#S8749; CAS#2097938-73-1\nMdivi-1 SelleckChem Cat#S7162; CAS#338967-87-6\nMidostaurin SelleckChem Cat#S8064; CAS#120685-11-2\nMK-2206 2HCl SelleckChem Cat#S1078; CAS#1032350-13-2\nML141 SelleckChem Cat#S7686; CAS#71203-35-5\nNSC319276 SelleckChem Cat#S7149; CAS#71555-25-4\nNVP-BEP800 SelleckChem Cat#S1498; CAS#847559-80-2\nPalbociclib (PD-0332991) HCl SelleckChem Cat#S1116; CAS#827022-32-2\nPF-03814735 SelleckChem Cat#S2725; CAS#942487-16-3\nPF-3758309 SelleckChem Cat#S7094; CAS#898044-15-0\nPHA-793887 SelleckChem Cat#S1487; CAS#718630-59-2\nPictilisib SelleckChem Cat#S1065; CAS#957054-30-7\nPKR Inhibitor Cayman Chemical Cat#15323; CAS#608512-97-6\nQNZ (EVP4593) SelleckChem Cat#S4902; CAS#545380-34-5\nR-406 SelleckChem Cat#S2194; CAS#841290-81-1\nR-547 SelleckChem Cat#S2688; CAS#741713-40-6\nRapamycin SelleckChem Cat#S1039; CAS#53123-88-9\nRavoxertinib SelleckChem Cat#S7554; CAS#1453848-26-4\nRemdesivir BioVision Cat#B2997; CAS#1809249-37-3\nRipasudil (K-115) hydrochloride dihydrate SelleckChem Cat#S7995; CAS#887375-67-9\nRomidepsin (FK228, Depsipeptide) SelleckChem Cat#S3020; CAS#128517-07-7\nRuboxistaurin HCl(LY333531) SelleckChem Cat#S7663; CAS#169939-93-9\nSapanisertib SelleckChem Cat#S2811; CAS#1224844-38-5\nSAR-407899 Cayman Chemical Cat#21717; CAS#923359-38-0\nSB743921 HCl SelleckChem Cat#S2182; CAS#940929-33-9\nSGI-1776 free base SelleckChem Cat#S2198; CAS#1025065-69-3\nSilmitasertib SelleckChem Cat#S2248; CAS#1009820-21-6\nSorafenib Tosylate SelleckChem Cat#S1040; CAS#475207-59-1\nSotrastaurin SelleckChem Cat#S2791; CAS#425637-18-9\nStattic SelleckChem Cat#S7024; CAS#19983-44-9\nStaurosporine SelleckChem Cat#S1421; CAS#62996-74-1\nTanzisertib SelleckChem Cat#S8490; CAS#899805-25-5(freebase)\nTasquinimod SelleckChem Cat#S7617; CAS#254964-60-8\nTHZ1 2HCl SelleckChem Cat#S7549; CAS#1604810-83-4(freebase)\nTpl2 Kinase Inhibitor 1 Cayman Chemical Cat#19710; CAS#871307-18-5\nU73122 SelleckChem Cat#S8011; CAS#112648-68-7\nVolasertib SelleckChem Cat#S2235; CAS#755038-65-4\nXL413 (BMS-863233) SelleckChem Cat#S7547; CAS#1169562-71-3\nY-39983 HCl SelleckChem Cat#S7935; CAS#173897-44-4\nCCL2/MCP-1, Capture Antibody R\u0026D Systems Cat#MAB679\nCCL5/RANTES, Capture Antibody R\u0026D Systems Cat#MAB678\nCCL11/Eotaxin, Capture Antibody R\u0026D Systems Cat#MAB320\nGM-CSF, Capture Antibody R\u0026D Systems Cat#MAB615\nIL-1RA, Capture Antibody Peprotech Cat#500-P209\nCCL13/MCP-4, Capture Antibody R\u0026D Systems Cat#MAB327\nIL-4, Capture Antibody R\u0026D Systems Cat#MAB604\nIL-10, Capture Antibody Peprotech Cat#500-P20\nIL-15, Capture Antibody R\u0026D Systems Cat#MAB647\nIL-1beta, Capture Antibody R\u0026D Systems Cat#MAB601\nCCL8/MCP-2, Capture Antibody Peprotech Cat#500-P35\nCXCL9/MIG, Capture Antibody Peprotech Cat#500-P50\nCCL3/MIP-1alpha, Capture Antibody R\u0026D Systems Cat#MAB670\nCXCL2/GRO-Beta, Capture Antibody Peprotech Cat#500-P104\nTGF-Beta1, Capture Antibody R\u0026D Systems Cat#MAB240\nCXCL16, Capture Antibody Peprotech Cat#500-P200\nCXCL8/IL-8, Capture Antibody R\u0026D Systems Cat#MAB208\nMMP-9, Capture Antibody R\u0026D Systems Cat#MAB936\nCXCL1/GRO-alpha, Capture Antibody Peprotech Cat#500-P92\nIL-7, Capture Antibody R\u0026D Systems Cat#MAB207\nCCL4/MIP-1beta, Capture Antibody R\u0026D Systems Cat#MAB271\nIL-1alpha, Capture Antibody R\u0026D Systems Cat#MAB200\nIL-12 (p70), Capture Antibody Peprotech Cat#500-P154G\nIL-16, Capture Antibody R\u0026D Systems Cat#MAB316\nCCL20/MIP-3a, Capture Antibody R\u0026D Systems Cat#MAB360\nTNF-alpha, Capture Antibody R\u0026D Systems Cat#MAB610\nTrappin-2/Elafin, Capture Antibody R\u0026D Systems Cat#AF1747\nIL-17A, Capture Antibody R\u0026D Systems Cat#MAB317\nCXCL10/IP-10, Capture Antibody R\u0026D Systems Cat#MAB266\nS100A8, Capture Antibody R\u0026D Systems Cat#DS8900\nIL-22, Capture Antibody Peprotech Cat#500-P211\nCXCL5/ENA-78, Capture Antibody R\u0026D Systems Cat#MAB654\nIL-6, Capture Antibody R\u0026D Systems Cat#MAB206\nCCL7/MCP-3, Capture Antibody R\u0026D Systems Cat#MAB282\nCCL2/MCP-1, Protein std R\u0026D Systems Cat#279-MC\nCCL5/RANTES, Protein std R\u0026D Systems Cat#278-RN\nCCL11/Eotaxin, Protein std Peprotech Cat#300-21\nGM-CSF, Protein std R\u0026D Systems Cat#215-GM\nIL-1RA, Protein std Peprotech Cat#200-01RA\nCCL13/MCP-4, Protein std R\u0026D Systems Cat#327-P4\nIL-4, Protein std R\u0026D Systems Cat#204-IL\nIL-10, Protein std Peprotech Cat#200-10\nIL-15, Protein std R\u0026D Systems Cat#247-ILB\nIL-1beta, Protein std R\u0026D Systems Cat#201-LB\nCCL8/MCP-2, Protein std Peprotech Cat#300-15\nCXCL9/MIG, Protein std R\u0026D Systems Cat#392-MG\nCCL3/MIP-1alpha, Protein std R\u0026D Systems Cat#270-LD\nCXCL2/GRO-Beta, Protein std Peprotech Cat#300-39\nTGF-Beta1, Protein std Peprotech Cat#100-21\nCXCL16, Protein std Peprotech Cat#300-55\nCXCL8/IL-8, Protein std R\u0026D Systems Cat#208-IL\nMMP-9, Protein std R\u0026D Systems Cat#911-MP\nCXCL1/GRO-alpha, Protein std Peprotech Cat#300-11\nIL-7, Protein std R\u0026D Systems Cat#207-IL\nCCL4/MIP-1beta, Protein std R\u0026D Systems Cat#271-BME\nIL-1alpha, Protein std Peprotech Cat#200-01A\nIL-12(p70), Protein std R\u0026D Systems Cat#219-IL\nIL-16, Protein std Peprotech Cat#200-16\nCCL20/MIP-3a, Protein std Peprotech Cat#300-29A\nTNF-alpha, Protein std R\u0026D Systems Cat#210-TA\nTrappin-2/Elafin, Protein std R\u0026D Systems Cat#1747-PI\nIL-17A, Protein std Peprotech Cat#200-17\nCXCL10/IP-10, Protein std R\u0026D Systems Cat#266-IP\nS100A8, Protein std R\u0026D Systems Cat#DS8900\nIL-22, Protein std Peprotech Cat#200-22\nCXCL5/ENA-78, Protein std R\u0026D Systems Cat#254-XB\nIL-6, Protein std R\u0026D Systems Cat#206-IL\nCCL7/MCP-3, Protein std R\u0026D Systems Cat#282-P3\nCCL2/MCP-1, Detection Antibody R\u0026D Systems Cat#BAF279\nCCL5/RANTES, Detection Antibody R\u0026D Systems Cat#BAF278\nCCL11/Eotaxin, Detection Antibody R\u0026D Systems Cat#BAF320\nGM-CSF, Detection Antibody R\u0026D Systems Cat#BAM 215\nIL-1RA, Detection Antibody Peprotech Cat#500-P209BT\nCCL13/MCP-4, Detection Antibody R\u0026D Systems Cat#BAF327\nIL-4, Detection Antibody R\u0026D Systems Cat#BAF204\nIL-10, Detection Antibody Peprotech Cat#500-P20BT\nIL-15, Detection Antibody R\u0026D Systems Cat#BAM 247\nIL-1beta, Detection Antibody R\u0026D Systems Cat#BAF201\nCCL8/MCP-2, Detection Antibody Peprotech Cat#500-P35BT\nCXCL9/MIG, Detection Antibody Peprotech Cat#500-P50BT\nCCL3/MIP-1alpha, Detection Antibody R\u0026D Systems Cat#BAF270\nCXCL2/GRO-Beta, Detection Antibody Peprotech Cat#500P104BT\nTGF-Beta1, Detection Antibody R\u0026D Systems Cat#BAM 2462\nCXCL16, Detection Antibody Peprotech Cat#500-P200BT\nCXCL8/IL-8, Detection Antibody R\u0026D Systems Cat#BAF208\nMMP-9, Detection Antibody R\u0026D Systems Cat#BAF911\nCXCL1/GRO-alpha, Detection Antibody Peprotech Cat#500P92BT\nIL-7, Detection Antibody R\u0026D Systems Cat#BAF207\nCCL4/MIP-1beta, Detection Antibody R\u0026D Systems Cat#BAF271\nIL-1alpha, Detection Antibody R\u0026D Systems Cat#BAF200\nIL-12(p70), Detection Antibody Peprotech Cat#500-P154GBT\nIL-16, Detection Antibody R\u0026D Systems Cat#BAF316\nCCL20/MIP-3a, Detection Antibody R\u0026D Systems Cat#BAF360\nTNF-alpha, Detection Antibody R\u0026D Systems Cat#BAF210\nTrappin-2/Elafin, Detection Antibody R\u0026D Systems Cat#BAF1747\nIL-17A, Detection Antibody R\u0026D Systems Cat#BAF317\nCXCL10/IP-10, Detection Antibody Peprotech Cat#500-P93BT\nS100A8, Detection Antibody R\u0026D Systems Cat#DS8900\nIL-22, Detection Antibody Peprotech Cat#500-P211BT\nCXCL5/ENA-78, Detection Antibody R\u0026D Systems Cat#BAF254\nIL-6, Detection Antibody R\u0026D Systems Cat#BAF206\nCCL7/MCP-3, Detection Antibody R\u0026D Systems Cat#BAF282\nCritical Commercial Assays\nMTT assay Roche Cat#11465007001\nLuna Universal One-Step RT-qPCR Kit New England Biolabs Cat#E3005L\nCellTiter-Glo Luminescent Cell Viability Assay Promega Cat#G7570\nDirect-zol RNA Miniprep Plus kit Zymo Research Cat#R2072\nKAPA SYBR FAST qPCR Master Mix Roche Cat#07959389001\nBio-Rad II Protein Assay Kit Bio-Rad Cat#5000002\nDeposited Data\nPhosphoproteomics data of SARS-CoV-2 infected Vero E6 cells This paper PRIDE Project ID: PXD019113\nSupplemental Tables in Mendeley Data This paper https://dx.doi.org/10.17632/dpkbh2g9hy.1\nCORUM v3.0 Giurgiu et al., 2019 http://mips.helmholtz-muenchen.de/corum/\nRNA-seq dataset for transcription factor activities Blanco-Melo et al., 2020 GSE147507\nPhosphoproteomics datasets of biological conditions Ochoa et al., 2016 https://www.embopress.org/doi/full/10.15252/msb.20167295\nFunctional scores for phosphorylation sites Ochoa et al., 2020 https://idp.nature.com/authorize?response_type=cookie\u0026client_id=grover\u0026redirect_uri=https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41587-019-0344-3\nGene identifier mapping database from BioMart Ensembl http://uswest.ensembl.org/biomart/martview/5ccd994c794265409f21c6194730ce5b\nMolecular Signatures Database for gene set enrichment analysis Subramanian et al., 2005 https://www.gsea-msigdb.org/gsea/msigdb/index.jsp\nKinase-substrate relationships Bachman et al., 2019 https://www.biorxiv.org/content/10.1101/822668v3.full\nChlorocebus proteome sequences for peptide searches Uniprot https://www.uniprot.org/proteomes/UP000029965\nSars-CoV-2 genomic sequences (hCoV-19/France/IDF0372/2020) GISAID Accession number EPI_ISL_406596\nExperimental Models: Cell Lines\nACE2-A549 human lung carcinoma Donated from the laboratory of Brad Rosenberg N/A\nCaco-2 ATCC Cat#HTB-37\nVERO C1008 [Vero 76, clone E6, Vero E6] (Vero E6) ATCC Cat#CRL-1586\nHEK293T/17 cells ATCC Cat#CRL-11268\nOligonucleotides\nON-TARGETplus Human MAPK12 (6300) siRNA - SMARTpool, 5 nmol Horizon Discovery/Dharmacon Cat#L-003590-00-0005\nON-TARGETplus Human MAPK13 (5603) siRNA - SMARTpool, 5 nmol Horizon Discovery/Dharmacon Cat#L-003591-00-0005\nON-TARGETplus Human MAP2K3 (5606) siRNA - SMARTpool, 5 nmol Horizon Discovery/Dharmacon Cat#L-003509-00-0005\nON-TARGETplus Human ACE2 (59272) siRNA - SMARTpool Horizon Discovery/Dharmacon Cat#L-005755-00-0005\nN gene region (reverse) 5′-CGAAGGTGTGACTTCCATG-3′ Eurofins N/A\nN gene region (forward)5′-TAATCAGACAAGGAACTGATTA-3′ Eurofins N/A\nRecombinant DNA\npLVX-TetOne-Puro empty vector Takara Cat#631847\npLVX-TetOne-Puro-SARS-CoV-2-N-2xStrep This paper N/A\npMD2.G, Addgene Gift from Didier Trono Addgene Plasmid #12259\nGag-Pol-Tat-Rev packaging construct Gift from Judd Hultquist pJH045\nSoftware and Algorithms\nartMS Bioconductor https://www.bioconductor.org/packages/release/bioc/html/artMS.html\nMSstats Bioconductor https://www.bioconductor.org/packages/release/bioc/html/artMS.html\nThe R Project for Statistical Computing R Core Team, 2019 http://www.r-project.org/index.html\nSpectronaut Biognosys https://biognosys.com/shop/spectronaut\nZEN (Blue edition) Carl Zeiss Microscopy https://www.zeiss.com/zen\nSPPIDER v2 Porollo and Meller, 2007 http://sppider.cchmc.org/\nDoRothEA Garcia-Alonso et al., 2019 https://saezlab.github.io/dorothea/\nVIPER Alvarez et al., 2016 https://www.bioconductor.org/packages/release/bioc/html/viper.html\nBiostrings Bioconductor https://bioconductor.org/packages/release/bioc/html/Biostrings.html\nclusterProfiler Bioconductor 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