Purification:Article Title: Endogenous IFITMs boost SARS-coronavirus 1 and 2 replication whereas overexpression inhibits infection by relocalizing ACE2.
Article Snippet: .. Antibodies IRDye 680RD Goat anti-Rabbit IgG (H + L) LI-COR Cat926-68071 IRDye 800CW Goat anti-Mouse IgG (H + L) LI-COR Cat# 926-32210 IRDye 800RD Goat anti-Rat IgG (H + L) LI-COR Cat# 925-32219 HCoV-229E Nucleocapsid Antibody SinoBiological Cat# 40640-T62 Anti-Coronavirus NL63 Ingenasa M.30.HCo.I2D4 Anti-Coronavirus Antibody, OC-43 strain Millipore Cat# MAB9012 Purified anti-GAPDH Antibody Biolegend Cat# 607902 Rabbit polyclonal anti-IFITM1 Cell signaling Cat# 13126 S Rabbit polyclonal anti-IFITM2 Cell signaling Cat# 13530S Rabbit polyclonal anti-IFITM3 Cell signaling Cat# 59212S V5-Tag (E9H8O) Mouse mAb Cell signaling Cat# 80076 SARS-CoV-2 (2019-nCoV) Nucleocapsid Antibody SinoBiological Cat# 40588-MM124 Rabbit polyclonal anti-ACE2 Abcam Cat# ab15348 Mouse monoclonal anti-flag Sigma-Aldrich Cat# F1804 Fixable Viability Dye eFluor 780 Thermo Fisher Cat# 65-0865-14 Rabbit monoclonal Alexa Fluor 647 anti-CD46 Abcam Cat# 275208 Rat Monoclonal PerCP-Cy5.5 anti-CD4 Biolegend Cat# 317428 Bacterial and virus strains VSVDG(GFP)*VSV-G Klaus Conzelmann N/A hCoV-229E ATCC Cat# VR-740TM hCoV-NL63 Lia van der Hoek N/A hCoV-OC43 ATCC Cat# CR-1558TM Renilla hCoV-229E Volker Thiel N/A BetaCoV/Netherlands/01/NL/2020 European Virus Archive Cat# 010V 03903 VSVDG(GFP)*VSV-G Klaus Conzelmann N/A BetaCoV/Netherlands/01/NL/2020 European Virus Archive Cat# 010V 03903 BetaCoV/B.1.617.2/Delta Florian Schmidt (University of Bonn) N/A BetaCoV/Munich/BavPat1/2020 GISAID; Wölfel et al., 202047 EPI_ISL_406862 SARS-CoV (rSCV, Frankfurt-1 virus isolate) Pfefferle et al., 200929 Genbank accession no. AY310120 rMERS-CoV, MERS-CoV/EMC2012 Muth et al., 201748 Genbank accession no. NC_019843.3 Chemicals, peptides, and recombinant proteins L-Glutamine Pan Biotech Cat# P04-80100 DAPI Sigma-Aldrich Cat# D9542-1MG; CAS: 28718-90-3 Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat# 41965039 Dulbecco’s Phosphate Buffered Saline (PBS) Thermo Fisher Cat# 14190094 Minimum Essential Medium Eagle (MEM) Sigma-Aldrich Cat# M4655 Opti-MEM Gibco Cat# M3942 Roswell Park Memorial Institute (RPMI) Gibco Cat# 22400089 Penicillin-Streptomycin Thermo Fisher Cat# 15140122 non-essential amino acids Sigma-Aldrich Cat# M7145 (Continued on next page) iScience 26, 106395, April 21, 2023 17 .. Sodium pyruvate Sigma-Aldrich Cat# S8636 FCS Gibco Cat# 10270106 Trypsin EDTA Gibco Cat# T3924 Versene Thermo Fisher Cat# 15040066 TMB peroxidase substrate (Sure blue) Medac Cat# 52-00-04 BD Cytofix/Cytoperm Fixation/Permeabilization Solution Kit BD Biosciences Cat# 554714 Lipofectamine RNAiMAX ThermoFisher Cat# 13778075 SuperScript III Platinum One-Step qRT-PCR Kit Invitrogen Cat# 11732088 Renilla Luciferase Assay kit Promega Cat# E2810 Quick RNA Miniprep Kit ZYMO research Cat# R1055 QIAamp Viral RNA Kits QIAGEN Cat# 52906 Luciferase Assay Kit Promega Cat# E1500 Mowiol 4-88 ROTH Cat# 0713.1 Blocker Casein in PBS Thermo Fisher Cat# 37528 TaqMan Fast Virus 1-Step Master Mix ThermoFisher Cat# 4444436 Tween 20 Sigma-Aldrich Cat# P7949500ML Triton X-100 Sigma-Aldrich Cat#T9284 100ML GAPD (GAPDH) Endogenous Control ThermoFisher Cat# 4352338E b-Mercaptoethanol Sigma-Aldrich Cat# 444203 Immobilon-FL PVDF membranes Merck Millipore Cat# IPVH00010 Paraformaldehyde Merck, Darmstadt Cat# 104005 TransIT-LT1 Mirus Cat# MIR2300 NuPAGE 4G12% Bis-Tris Gels ThermoFisher Cat# NP0321BOX Synthetic SARS-CoV-2-RNA Twist Bioscience Cat# 102019 RNAiMAX ThermoFisher Cat# LMRNA015 Recombinant IFN-a2 pbl assay science Cat# 11101-1 Recombinant IFN-b R&D systems Cat# 8499-IF-010 Recombinant IFN-g Sigma-Aldrich Cat# I3265 Recombinant IFN- l3 CHO Cat# 5259-IL-025 Cytochalasin D ThermoFisher Cat# PHZ1063 Agarose Sigma-Aldrich Cat# A9539 Experimental models: Cell lines Human: Calu-3 ATCC or M. Frick Cat# HTB-55 or N/A Human: Caco2 Holger Barth Human: Huh7.5 Ralf Bartenschlager Human: Huh7 Anna-Laura Kretz LLCMK2 by Lia van der Hoek
Article Title: Extracellular vesicles from alveolar macrophages harboring phagocytosed methicillin-resistant Staphylococcus aureus induce necroptosis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-Phospho-RIPK3 Abcam Cat# ab222320; RRID: AB_2868434 Rabbit anti-Phospho-MLKL Abcam Cat# ab196436; RRID: AB_2687465 Rabbit anti-GSDMD Abcam Cat# ab209845; RRID: AB_2783550 Rabbit anti-CD63 Abcam Cat# ab217345; RRID: AB_2754982 Rabbit anti-Caspase1 Abcam Cat# ab179515; RRID: AB_2884954 Rabbit anti-ApoA1 Abcam Cat# ab300085 Rabbit anti-TSG101 ABclonal Cat# A5789; RRID: AB_2863517 Rabbit anti-TRAF6 ABclonal Cat# A16991; RRID: AB_2772697 Rabbit anti-CD9 ABclonal Cat# A1703; RRID: AB_2763755 Rabbit anti-Caspase 7 Abways Cat# CY5579 Rabbit anti-CD81 Affinity Cat# DF2306; RRID: AB_2839530 Rabbit anti-Phospho-RIPK1 Cell Signaling Technology Cat# 53286; RRID: AB_2925183 Rabbit anti-RIPK1 Cell Signaling Technology Cat# 3493; RRID: AB_2305314 Rabbit anti-RIPK3 Cell Signaling Technology Cat# 95702; RRID: AB_2721823 Rabbit anti-MLKL Cell Signaling Technology Cat# 37705; RRID: AB_2799118 Rabbit anti-TNF-a Cell Signaling Technology Cat# 11948; RRID: AB_2687962 Rabbit anti-Caspase3 Cell Signaling Technology Cat# 9662; RRID: AB_331439 Rabbit anti-Caspase8 Cell Signaling Technology Cat# 4790; RRID: AB_10545768 Rabbit anti-Flag Cell Signaling Technology Cat#14793; RRID: AB_2572291 Mouse anti-GAPDH Proteintech Cat# 60004-1-lg; RRID: AB_2919223 Goat anti-mouse lgG Absin Cat# abs20039; RRID: AB_3076309 Goat anti-rabbit lgG Absin Cat# abs20040; RRID: AB_2938713 Anti-mouse F4/80 Biolegend Cat# 123115; RRID: AB_893493 Anti-mouse Siglec-F Biolegend Cat# 155505; RRID: AB_2750235 Anti-mouse CD11b Biolegend Cat# 101212; RRID: AB_312795 Anti-mouse Ly6G Biolegend Cat# 127641; RRID: AB_2565881 Anti-mouse CD63 Biolegend Cat# 143905; RRID: AB_2565495 Rabbit anti-F4/80 Abcam Cat# ab300421; RRID: AB_2936298 Rabbit anti-p-MLKL Cell Signaling Technology Cat# 37333; RRID: AB_2799112 Rabbit anti- Prosurfactant Protein C Abcam Cat# ab211326; RRID: AB_2927746 Purified anti-CD9 Antibody Biolegend Cat# 124802; RRID: AB_1279332 iFluorTM 488 Conjugated goat anti-rabbit lgG Huabio Cat# HA1121 iFluorTM 594 Conjugated goat anti-rabbit lgG Huabio Cat# HA1122 iFluorTM 488 Phalloidin Yeasen Cat# 40736 Bacterial and virus strains USA300 ATCC Cat# BAA-1556 S. aureus ATCC Cat# 25923 Chemicals, peptides, and recombinant proteins DAPI Vector Cat# H-1200 Dynamin IN MedChemExpress Cat# HY-152215 FBS Gibco Cat# 10099158 GW4869 MedChemExpress Cat# HY-19363 INTERFERin Polyplus Transfection Cat# #382 (Continued on next page) Cell Reports 43, 114453, July 23, 2024 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Jetpei Polyplus Transfection Cat# #499 Latex beads Invitrogen Cat# A37304 Nonfat powdered milk Sangon Biotech Cat# A600669-0250 O. C. T Compound SAKURA Cat# 4583 Protease inhibitors Beyotime Cat# P1005 PKH26 Sigma Cat# MID126 Proteinase K MCE Cat# HY-108717 Recombinant mouse TNF-a ABclonal Cat# RP01702 RIPA lysis buffer Beyotime Cat# P0013E Red blood cell lysis buffer Solarbio Cat# R1010 RNase Solarbio Cat# R1030 SYBR Vazyme Cat# Q121-02 TNF-a antagonist MedChemExpress Cat# HY-110203 Type II collagenase Worthington Biochemical Cat# LS004177 RNAiso Plus Takara Cat# 9108 Vancomycin Sangon Biotech Cat# A600983 Critical commercial assays Annexin V-APC/PI Apoptosis Kit Multi Sciences Cat# AT107 CCK-8 Kit Fdbio Cat# FD3788 DABtunel Kit Haokebio Cat# HKI0012 Enhanced Chemiluminescence Substrate Kit NCM Biotech Cat# P10300 Gaussia Luciferase Assay Kit Beyotime Cat# RG021S HiFiScript cDNA Synthesis Kit CWBIO Cat# CW2569 Hairpin-itTM microRNA and U6 snRNA Normalization RT-PCR Quantitation Kit GenePharma Cat# E22001 PierceTM BCA Protein Assay Kit Thermo Fisher Cat# 23225 mmu-IL-1b ELISA Kit Abcam Cat# ab197742 mmu-IL-6 ELISA Kit Abcam Cat# ab222503 mmu-TNF-a ELISA Kit Abcam Cat# ab208348 Deposited data Proteomics data This paper iProX: PXD052452 miRNA-seq data This paper NCBI: PRJNA1113992 Experimental models: Cell lines MH-S cells ATCC ATCC CRL-2019 MLE12 cells ATCC ATCC CRL-2110 Experimental models: Organisms/strains Mouse: C57BL/6J Shanghai SLAC Laboratory Animal Co., Ltd. (Shanghai, China) N/A Oligonucleotides Primers for real-time PCR, see Table S1 This paper N/A miRNA mimics, see Table S1 This paper N/A siRNA, see Table S1 This paper N/A Recombinant DNA TRAF6 plasmid Miaoling Biology P19727 Wild-type pmir-GLO luciferase plasmids of TRAF6 3’ untranslated region GenePharma N/A Mutant pmir-GLO luciferase plasmids of TRAF6 3’ untranslated region GenePharma N/A (Continued on next page) 20 Cell Reports 43, 114453, July 23, 2024
Virus:Article Title: Endogenous IFITMs boost SARS-coronavirus 1 and 2 replication whereas overexpression inhibits infection by relocalizing ACE2.
Article Snippet: .. Antibodies IRDye 680RD Goat anti-Rabbit IgG (H + L) LI-COR Cat926-68071 IRDye 800CW Goat anti-Mouse IgG (H + L) LI-COR Cat# 926-32210 IRDye 800RD Goat anti-Rat IgG (H + L) LI-COR Cat# 925-32219 HCoV-229E Nucleocapsid Antibody SinoBiological Cat# 40640-T62 Anti-Coronavirus NL63 Ingenasa M.30.HCo.I2D4 Anti-Coronavirus Antibody, OC-43 strain Millipore Cat# MAB9012 Purified anti-GAPDH Antibody Biolegend Cat# 607902 Rabbit polyclonal anti-IFITM1 Cell signaling Cat# 13126 S Rabbit polyclonal anti-IFITM2 Cell signaling Cat# 13530S Rabbit polyclonal anti-IFITM3 Cell signaling Cat# 59212S V5-Tag (E9H8O) Mouse mAb Cell signaling Cat# 80076 SARS-CoV-2 (2019-nCoV) Nucleocapsid Antibody SinoBiological Cat# 40588-MM124 Rabbit polyclonal anti-ACE2 Abcam Cat# ab15348 Mouse monoclonal anti-flag Sigma-Aldrich Cat# F1804 Fixable Viability Dye eFluor 780 Thermo Fisher Cat# 65-0865-14 Rabbit monoclonal Alexa Fluor 647 anti-CD46 Abcam Cat# 275208 Rat Monoclonal PerCP-Cy5.5 anti-CD4 Biolegend Cat# 317428 Bacterial and virus strains VSVDG(GFP)*VSV-G Klaus Conzelmann N/A hCoV-229E ATCC Cat# VR-740TM hCoV-NL63 Lia van der Hoek N/A hCoV-OC43 ATCC Cat# CR-1558TM Renilla hCoV-229E Volker Thiel N/A BetaCoV/Netherlands/01/NL/2020 European Virus Archive Cat# 010V 03903 VSVDG(GFP)*VSV-G Klaus Conzelmann N/A BetaCoV/Netherlands/01/NL/2020 European Virus Archive Cat# 010V 03903 BetaCoV/B.1.617.2/Delta Florian Schmidt (University of Bonn) N/A BetaCoV/Munich/BavPat1/2020 GISAID; Wölfel et al., 202047 EPI_ISL_406862 SARS-CoV (rSCV, Frankfurt-1 virus isolate) Pfefferle et al., 200929 Genbank accession no. AY310120 rMERS-CoV, MERS-CoV/EMC2012 Muth et al., 201748 Genbank accession no. NC_019843.3 Chemicals, peptides, and recombinant proteins L-Glutamine Pan Biotech Cat# P04-80100 DAPI Sigma-Aldrich Cat# D9542-1MG; CAS: 28718-90-3 Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat# 41965039 Dulbecco’s Phosphate Buffered Saline (PBS) Thermo Fisher Cat# 14190094 Minimum Essential Medium Eagle (MEM) Sigma-Aldrich Cat# M4655 Opti-MEM Gibco Cat# M3942 Roswell Park Memorial Institute (RPMI) Gibco Cat# 22400089 Penicillin-Streptomycin Thermo Fisher Cat# 15140122 non-essential amino acids Sigma-Aldrich Cat# M7145 (Continued on next page) iScience 26, 106395, April 21, 2023 17 .. Sodium pyruvate Sigma-Aldrich Cat# S8636 FCS Gibco Cat# 10270106 Trypsin EDTA Gibco Cat# T3924 Versene Thermo Fisher Cat# 15040066 TMB peroxidase substrate (Sure blue) Medac Cat# 52-00-04 BD Cytofix/Cytoperm Fixation/Permeabilization Solution Kit BD Biosciences Cat# 554714 Lipofectamine RNAiMAX ThermoFisher Cat# 13778075 SuperScript III Platinum One-Step qRT-PCR Kit Invitrogen Cat# 11732088 Renilla Luciferase Assay kit Promega Cat# E2810 Quick RNA Miniprep Kit ZYMO research Cat# R1055 QIAamp Viral RNA Kits QIAGEN Cat# 52906 Luciferase Assay Kit Promega Cat# E1500 Mowiol 4-88 ROTH Cat# 0713.1 Blocker Casein in PBS Thermo Fisher Cat# 37528 TaqMan Fast Virus 1-Step Master Mix ThermoFisher Cat# 4444436 Tween 20 Sigma-Aldrich Cat# P7949500ML Triton X-100 Sigma-Aldrich Cat#T9284 100ML GAPD (GAPDH) Endogenous Control ThermoFisher Cat# 4352338E b-Mercaptoethanol Sigma-Aldrich Cat# 444203 Immobilon-FL PVDF membranes Merck Millipore Cat# IPVH00010 Paraformaldehyde Merck, Darmstadt Cat# 104005 TransIT-LT1 Mirus Cat# MIR2300 NuPAGE 4G12% Bis-Tris Gels ThermoFisher Cat# NP0321BOX Synthetic SARS-CoV-2-RNA Twist Bioscience Cat# 102019 RNAiMAX ThermoFisher Cat# LMRNA015 Recombinant IFN-a2 pbl assay science Cat# 11101-1 Recombinant IFN-b R&D systems Cat# 8499-IF-010 Recombinant IFN-g Sigma-Aldrich Cat# I3265 Recombinant IFN- l3 CHO Cat# 5259-IL-025 Cytochalasin D ThermoFisher Cat# PHZ1063 Agarose Sigma-Aldrich Cat# A9539 Experimental models: Cell lines Human: Calu-3 ATCC or M. Frick Cat# HTB-55 or N/A Human: Caco2 Holger Barth Human: Huh7.5 Ralf Bartenschlager Human: Huh7 Anna-Laura Kretz LLCMK2 by Lia van der Hoek
Article Title: Novel methodologies for host-microbe interactions and microbiome-targeted therapeutics in 3D organotypic skin models.
Article Snippet: .. Antibodies (Supplemental Table S2) Mouse monoclonal anti‐Filaggrin (clone FLG01) Thermo Fisher Scientific Cat#FLG01‐1 RRID:AB 2894828 Rabbit monoclonal anti‐Ki67 (clone SP6) Abcam Cat#ab16667, RRID:AB 302459 Mouse monoclonal anti‐Involucrin (clone Mon150) [48] N/A Mouse monoclonal anti‐Keratin 10 (clone DE‐K10) Abcam Cat# ab9026 RRID:AB 306950 Rabbit monoclonal anti‐SKALP/Elafin (clone 92‐1) [49] N/A Goat polyclonal anti‐ hBD2 Abcam Cat# ab9871, RRID:AB 296681 Bacterial and virus strains (Supplemental Table S3) Cutibacterium acnes ATCC ATCC‐6919 Staphylococcus epidermidis ATCC ATCC‐12228 Staphylococcus capitis Clinical isolate N/A Corynebacterium aurimucosum Clinical isolate N/A Staphylococcus aureus ATCC ATCC‐29213 Staphylococcus aureus Clinical isolate from AD skin (SA‐ DUS‐011) N/A Biological samples .. Chemicals CnT‐Prime Epithelial Proliferation Medium CELLnTEC Cat#CnT‐PR CnT‐Prime 3D Barrier Culture Medium CELLnTEC Cat#CnT‐PR‐3D
Article Title: Vimentin inhibits type I interferon production by disrupting the TBK1-IKKε-IRF3 axis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-Flag-Rabbit SIGMA Cat#F7425-2MG; RRID: AB-2572291 anti-LaminB-Rabbit Solarbio Cat# K106482P- anti-HSV-1 Abcam Cat# ab6506 anti-IFNAR1-Rabbit Abcam Cat# ab124764 anti-Flag-Mouse SIGMA Cat# F1804-1MG anti-HA-Rabbit SIGMA Cat# SAB4300603 anti-HA-Mouse SIGMA Cat# HS658-2ML anti-GFP-Rabbit Proteintech Cat# 50430-2-AP anti-Vimentin-Rabbit Cell Signaling Technology Cat# 5741S anti-Vimentin-Mouse Abcam Cat#ab20346 anti-IRF3 Cell Signaling Technology Cat#4302; RRID: AB-1904036 anti-IRF3 phosphorylated at S396 Cell Signaling Technology Cat#4947; RRID: AB-823547 anti-TBK1 Cell Signaling Technology Cat#3504; RRID: AB-2255663 anti-TBK1 phosphorylated at S172 Cell Signaling Technology Cat#5483 anti-GAPDH Proteintech Group Cat#60004-1-Ig; RRID: AB-2107436 Anti-IKKε RD systems Cat#MAB3199 Alexa Flour 488 goat anti-rabbit IgG(H + L) Invitrogen Cat#A11008 Alexa Flour 633 goat anti-rabbit IgG(H + L) Invitrogen Cat#A21071 Alexa Flour 633 goat anti-mouse IgG(H + L) Invitrogen Cat#A21052 Alexa Flour 594 goat anti-mouse IgG(H + L) Invitrogen Cat#A11032 IRDye 800CW Goat anti-rabbit IgG (H + L) LI-COR Cat#926-32211 IRDye 800CW Goat anti-mouse IgG (H + L) LI-COR Cat#926-32210 Bacterial and virus strains The Sendai/Cantell strain ATCC ATCC VR-907 VSV-GFP Harbin Veterinary Research Institute N/A VSV-GFP Harbin Veterinary Research Institute N/A HSV-1-GFP Harbin Veterinary Research Institute N/A EMCV (HB10); GeneBank: JQ864080.1 Isolated from Pig N/A ADV Hanbio Biotechnology Co., Ltd. N/A Chemicals, peptides, and recombinant proteins anti-Flag (M2) beads Sigma-Aldrich Cat#M8823 Protein agarose A/G Santa Cruz Biotechnology Cat#20397 TRIzol reagent Invitrogen Cat#15596026 Poly(I:C) Sigma-Aldrich Cat#P1530 cGAMP Sigma-Aldrich Cat#SML1232-1EA Poly (dA:dT) Sigma-Aldrich Cat#P0883-10UN ISD Invitrogen Cat#tlrl-isdn protease inhibitor Cocktail Roche Cat#4693132001 Dulbecco’s Modified Eagle’s Medium (DMEM) GIBCO Cat#C11995500CP RPMI 1640 medium GIBCO Cat#C11875500CP fetal bovine serum (FBS) GIBCO Cat#10091-148 (Continued on next page) e1 Cell Reports 41, 111469, October 11, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Penicillin-Streptomycin Solution Hyclone Cat#SV30010 thioglycollate MERCK Cat#1.08191 Critical commercial assays Dual-Luciferase Reporter Assay System Promega Cat#E1910 PrimeScriptTM RT Reagent Kit Takara Cat# RR037A SYBR Premix Ex TaqTM II Takara Cat#RR820A Experimental models: Cell lines RAW264.7 RAW264.7 RAW264.7
Article Title: Extracellular vesicles from alveolar macrophages harboring phagocytosed methicillin-resistant Staphylococcus aureus induce necroptosis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-Phospho-RIPK3 Abcam Cat# ab222320; RRID: AB_2868434 Rabbit anti-Phospho-MLKL Abcam Cat# ab196436; RRID: AB_2687465 Rabbit anti-GSDMD Abcam Cat# ab209845; RRID: AB_2783550 Rabbit anti-CD63 Abcam Cat# ab217345; RRID: AB_2754982 Rabbit anti-Caspase1 Abcam Cat# ab179515; RRID: AB_2884954 Rabbit anti-ApoA1 Abcam Cat# ab300085 Rabbit anti-TSG101 ABclonal Cat# A5789; RRID: AB_2863517 Rabbit anti-TRAF6 ABclonal Cat# A16991; RRID: AB_2772697 Rabbit anti-CD9 ABclonal Cat# A1703; RRID: AB_2763755 Rabbit anti-Caspase 7 Abways Cat# CY5579 Rabbit anti-CD81 Affinity Cat# DF2306; RRID: AB_2839530 Rabbit anti-Phospho-RIPK1 Cell Signaling Technology Cat# 53286; RRID: AB_2925183 Rabbit anti-RIPK1 Cell Signaling Technology Cat# 3493; RRID: AB_2305314 Rabbit anti-RIPK3 Cell Signaling Technology Cat# 95702; RRID: AB_2721823 Rabbit anti-MLKL Cell Signaling Technology Cat# 37705; RRID: AB_2799118 Rabbit anti-TNF-a Cell Signaling Technology Cat# 11948; RRID: AB_2687962 Rabbit anti-Caspase3 Cell Signaling Technology Cat# 9662; RRID: AB_331439 Rabbit anti-Caspase8 Cell Signaling Technology Cat# 4790; RRID: AB_10545768 Rabbit anti-Flag Cell Signaling Technology Cat#14793; RRID: AB_2572291 Mouse anti-GAPDH Proteintech Cat# 60004-1-lg; RRID: AB_2919223 Goat anti-mouse lgG Absin Cat# abs20039; RRID: AB_3076309 Goat anti-rabbit lgG Absin Cat# abs20040; RRID: AB_2938713 Anti-mouse F4/80 Biolegend Cat# 123115; RRID: AB_893493 Anti-mouse Siglec-F Biolegend Cat# 155505; RRID: AB_2750235 Anti-mouse CD11b Biolegend Cat# 101212; RRID: AB_312795 Anti-mouse Ly6G Biolegend Cat# 127641; RRID: AB_2565881 Anti-mouse CD63 Biolegend Cat# 143905; RRID: AB_2565495 Rabbit anti-F4/80 Abcam Cat# ab300421; RRID: AB_2936298 Rabbit anti-p-MLKL Cell Signaling Technology Cat# 37333; RRID: AB_2799112 Rabbit anti- Prosurfactant Protein C Abcam Cat# ab211326; RRID: AB_2927746 Purified anti-CD9 Antibody Biolegend Cat# 124802; RRID: AB_1279332 iFluorTM 488 Conjugated goat anti-rabbit lgG Huabio Cat# HA1121 iFluorTM 594 Conjugated goat anti-rabbit lgG Huabio Cat# HA1122 iFluorTM 488 Phalloidin Yeasen Cat# 40736 Bacterial and virus strains USA300 ATCC Cat# BAA-1556 S. aureus ATCC Cat# 25923 Chemicals, peptides, and recombinant proteins DAPI Vector Cat# H-1200 Dynamin IN MedChemExpress Cat# HY-152215 FBS Gibco Cat# 10099158 GW4869 MedChemExpress Cat# HY-19363 INTERFERin Polyplus Transfection Cat# #382 (Continued on next page) Cell Reports 43, 114453, July 23, 2024 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Jetpei Polyplus Transfection Cat# #499 Latex beads Invitrogen Cat# A37304 Nonfat powdered milk Sangon Biotech Cat# A600669-0250 O. C. T Compound SAKURA Cat# 4583 Protease inhibitors Beyotime Cat# P1005 PKH26 Sigma Cat# MID126 Proteinase K MCE Cat# HY-108717 Recombinant mouse TNF-a ABclonal Cat# RP01702 RIPA lysis buffer Beyotime Cat# P0013E Red blood cell lysis buffer Solarbio Cat# R1010 RNase Solarbio Cat# R1030 SYBR Vazyme Cat# Q121-02 TNF-a antagonist MedChemExpress Cat# HY-110203 Type II collagenase Worthington Biochemical Cat# LS004177 RNAiso Plus Takara Cat# 9108 Vancomycin Sangon Biotech Cat# A600983 Critical commercial assays Annexin V-APC/PI Apoptosis Kit Multi Sciences Cat# AT107 CCK-8 Kit Fdbio Cat# FD3788 DABtunel Kit Haokebio Cat# HKI0012 Enhanced Chemiluminescence Substrate Kit NCM Biotech Cat# P10300 Gaussia Luciferase Assay Kit Beyotime Cat# RG021S HiFiScript cDNA Synthesis Kit CWBIO Cat# CW2569 Hairpin-itTM microRNA and U6 snRNA Normalization RT-PCR Quantitation Kit GenePharma Cat# E22001 PierceTM BCA Protein Assay Kit Thermo Fisher Cat# 23225 mmu-IL-1b ELISA Kit Abcam Cat# ab197742 mmu-IL-6 ELISA Kit Abcam Cat# ab222503 mmu-TNF-a ELISA Kit Abcam Cat# ab208348 Deposited data Proteomics data This paper iProX: PXD052452 miRNA-seq data This paper NCBI: PRJNA1113992 Experimental models: Cell lines MH-S cells ATCC ATCC CRL-2019 MLE12 cells ATCC ATCC CRL-2110 Experimental models: Organisms/strains Mouse: C57BL/6J Shanghai SLAC Laboratory Animal Co., Ltd. (Shanghai, China) N/A Oligonucleotides Primers for real-time PCR, see Table S1 This paper N/A miRNA mimics, see Table S1 This paper N/A siRNA, see Table S1 This paper N/A Recombinant DNA TRAF6 plasmid Miaoling Biology P19727 Wild-type pmir-GLO luciferase plasmids of TRAF6 3’ untranslated region GenePharma N/A Mutant pmir-GLO luciferase plasmids of TRAF6 3’ untranslated region GenePharma N/A (Continued on next page) 20 Cell Reports 43, 114453, July 23, 2024
Article Title: Effective Search of Triterpenes with Anti-HSV-1 Activity Using a Classification Model by Logistic Regression
Article Snippet: .. The anti-HSV-1 assay conditions for these data included incubation times of 12–48 h and cell types of HeLa cells, Vero cells, and virus strains of mainly KOS (ATCC ® VR1493), Strain F (ATCC ® VR-733), and 17 (GenBank acc. no. NC_001,806) and HSV-1 MI (ATCC ® VR-539), which were acyclovir-sensitive strain. .. With the threshold of activity set to 25 μ M, 166 active and 250 inactive compounds were defined ( ); shows the results of the PCA of active or inactive compounds collected from ChEMBL, DNP, and the original papers using 267 descriptors.
Recombinant:Article Title: Endogenous IFITMs boost SARS-coronavirus 1 and 2 replication whereas overexpression inhibits infection by relocalizing ACE2.
Article Snippet: .. Antibodies IRDye 680RD Goat anti-Rabbit IgG (H + L) LI-COR Cat926-68071 IRDye 800CW Goat anti-Mouse IgG (H + L) LI-COR Cat# 926-32210 IRDye 800RD Goat anti-Rat IgG (H + L) LI-COR Cat# 925-32219 HCoV-229E Nucleocapsid Antibody SinoBiological Cat# 40640-T62 Anti-Coronavirus NL63 Ingenasa M.30.HCo.I2D4 Anti-Coronavirus Antibody, OC-43 strain Millipore Cat# MAB9012 Purified anti-GAPDH Antibody Biolegend Cat# 607902 Rabbit polyclonal anti-IFITM1 Cell signaling Cat# 13126 S Rabbit polyclonal anti-IFITM2 Cell signaling Cat# 13530S Rabbit polyclonal anti-IFITM3 Cell signaling Cat# 59212S V5-Tag (E9H8O) Mouse mAb Cell signaling Cat# 80076 SARS-CoV-2 (2019-nCoV) Nucleocapsid Antibody SinoBiological Cat# 40588-MM124 Rabbit polyclonal anti-ACE2 Abcam Cat# ab15348 Mouse monoclonal anti-flag Sigma-Aldrich Cat# F1804 Fixable Viability Dye eFluor 780 Thermo Fisher Cat# 65-0865-14 Rabbit monoclonal Alexa Fluor 647 anti-CD46 Abcam Cat# 275208 Rat Monoclonal PerCP-Cy5.5 anti-CD4 Biolegend Cat# 317428 Bacterial and virus strains VSVDG(GFP)*VSV-G Klaus Conzelmann N/A hCoV-229E ATCC Cat# VR-740TM hCoV-NL63 Lia van der Hoek N/A hCoV-OC43 ATCC Cat# CR-1558TM Renilla hCoV-229E Volker Thiel N/A BetaCoV/Netherlands/01/NL/2020 European Virus Archive Cat# 010V 03903 VSVDG(GFP)*VSV-G Klaus Conzelmann N/A BetaCoV/Netherlands/01/NL/2020 European Virus Archive Cat# 010V 03903 BetaCoV/B.1.617.2/Delta Florian Schmidt (University of Bonn) N/A BetaCoV/Munich/BavPat1/2020 GISAID; Wölfel et al., 202047 EPI_ISL_406862 SARS-CoV (rSCV, Frankfurt-1 virus isolate) Pfefferle et al., 200929 Genbank accession no. AY310120 rMERS-CoV, MERS-CoV/EMC2012 Muth et al., 201748 Genbank accession no. NC_019843.3 Chemicals, peptides, and recombinant proteins L-Glutamine Pan Biotech Cat# P04-80100 DAPI Sigma-Aldrich Cat# D9542-1MG; CAS: 28718-90-3 Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat# 41965039 Dulbecco’s Phosphate Buffered Saline (PBS) Thermo Fisher Cat# 14190094 Minimum Essential Medium Eagle (MEM) Sigma-Aldrich Cat# M4655 Opti-MEM Gibco Cat# M3942 Roswell Park Memorial Institute (RPMI) Gibco Cat# 22400089 Penicillin-Streptomycin Thermo Fisher Cat# 15140122 non-essential amino acids Sigma-Aldrich Cat# M7145 (Continued on next page) iScience 26, 106395, April 21, 2023 17 .. Sodium pyruvate Sigma-Aldrich Cat# S8636 FCS Gibco Cat# 10270106 Trypsin EDTA Gibco Cat# T3924 Versene Thermo Fisher Cat# 15040066 TMB peroxidase substrate (Sure blue) Medac Cat# 52-00-04 BD Cytofix/Cytoperm Fixation/Permeabilization Solution Kit BD Biosciences Cat# 554714 Lipofectamine RNAiMAX ThermoFisher Cat# 13778075 SuperScript III Platinum One-Step qRT-PCR Kit Invitrogen Cat# 11732088 Renilla Luciferase Assay kit Promega Cat# E2810 Quick RNA Miniprep Kit ZYMO research Cat# R1055 QIAamp Viral RNA Kits QIAGEN Cat# 52906 Luciferase Assay Kit Promega Cat# E1500 Mowiol 4-88 ROTH Cat# 0713.1 Blocker Casein in PBS Thermo Fisher Cat# 37528 TaqMan Fast Virus 1-Step Master Mix ThermoFisher Cat# 4444436 Tween 20 Sigma-Aldrich Cat# P7949500ML Triton X-100 Sigma-Aldrich Cat#T9284 100ML GAPD (GAPDH) Endogenous Control ThermoFisher Cat# 4352338E b-Mercaptoethanol Sigma-Aldrich Cat# 444203 Immobilon-FL PVDF membranes Merck Millipore Cat# IPVH00010 Paraformaldehyde Merck, Darmstadt Cat# 104005 TransIT-LT1 Mirus Cat# MIR2300 NuPAGE 4G12% Bis-Tris Gels ThermoFisher Cat# NP0321BOX Synthetic SARS-CoV-2-RNA Twist Bioscience Cat# 102019 RNAiMAX ThermoFisher Cat# LMRNA015 Recombinant IFN-a2 pbl assay science Cat# 11101-1 Recombinant IFN-b R&D systems Cat# 8499-IF-010 Recombinant IFN-g Sigma-Aldrich Cat# I3265 Recombinant IFN- l3 CHO Cat# 5259-IL-025 Cytochalasin D ThermoFisher Cat# PHZ1063 Agarose Sigma-Aldrich Cat# A9539 Experimental models: Cell lines Human: Calu-3 ATCC or M. Frick Cat# HTB-55 or N/A Human: Caco2 Holger Barth Human: Huh7.5 Ralf Bartenschlager Human: Huh7 Anna-Laura Kretz LLCMK2 by Lia van der Hoek
Article Title: Vimentin inhibits type I interferon production by disrupting the TBK1-IKKε-IRF3 axis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-Flag-Rabbit SIGMA Cat#F7425-2MG; RRID: AB-2572291 anti-LaminB-Rabbit Solarbio Cat# K106482P- anti-HSV-1 Abcam Cat# ab6506 anti-IFNAR1-Rabbit Abcam Cat# ab124764 anti-Flag-Mouse SIGMA Cat# F1804-1MG anti-HA-Rabbit SIGMA Cat# SAB4300603 anti-HA-Mouse SIGMA Cat# HS658-2ML anti-GFP-Rabbit Proteintech Cat# 50430-2-AP anti-Vimentin-Rabbit Cell Signaling Technology Cat# 5741S anti-Vimentin-Mouse Abcam Cat#ab20346 anti-IRF3 Cell Signaling Technology Cat#4302; RRID: AB-1904036 anti-IRF3 phosphorylated at S396 Cell Signaling Technology Cat#4947; RRID: AB-823547 anti-TBK1 Cell Signaling Technology Cat#3504; RRID: AB-2255663 anti-TBK1 phosphorylated at S172 Cell Signaling Technology Cat#5483 anti-GAPDH Proteintech Group Cat#60004-1-Ig; RRID: AB-2107436 Anti-IKKε RD systems Cat#MAB3199 Alexa Flour 488 goat anti-rabbit IgG(H + L) Invitrogen Cat#A11008 Alexa Flour 633 goat anti-rabbit IgG(H + L) Invitrogen Cat#A21071 Alexa Flour 633 goat anti-mouse IgG(H + L) Invitrogen Cat#A21052 Alexa Flour 594 goat anti-mouse IgG(H + L) Invitrogen Cat#A11032 IRDye 800CW Goat anti-rabbit IgG (H + L) LI-COR Cat#926-32211 IRDye 800CW Goat anti-mouse IgG (H + L) LI-COR Cat#926-32210 Bacterial and virus strains The Sendai/Cantell strain ATCC ATCC VR-907 VSV-GFP Harbin Veterinary Research Institute N/A VSV-GFP Harbin Veterinary Research Institute N/A HSV-1-GFP Harbin Veterinary Research Institute N/A EMCV (HB10); GeneBank: JQ864080.1 Isolated from Pig N/A ADV Hanbio Biotechnology Co., Ltd. N/A Chemicals, peptides, and recombinant proteins anti-Flag (M2) beads Sigma-Aldrich Cat#M8823 Protein agarose A/G Santa Cruz Biotechnology Cat#20397 TRIzol reagent Invitrogen Cat#15596026 Poly(I:C) Sigma-Aldrich Cat#P1530 cGAMP Sigma-Aldrich Cat#SML1232-1EA Poly (dA:dT) Sigma-Aldrich Cat#P0883-10UN ISD Invitrogen Cat#tlrl-isdn protease inhibitor Cocktail Roche Cat#4693132001 Dulbecco’s Modified Eagle’s Medium (DMEM) GIBCO Cat#C11995500CP RPMI 1640 medium GIBCO Cat#C11875500CP fetal bovine serum (FBS) GIBCO Cat#10091-148 (Continued on next page) e1 Cell Reports 41, 111469, October 11, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Penicillin-Streptomycin Solution Hyclone Cat#SV30010 thioglycollate MERCK Cat#1.08191 Critical commercial assays Dual-Luciferase Reporter Assay System Promega Cat#E1910 PrimeScriptTM RT Reagent Kit Takara Cat# RR037A SYBR Premix Ex TaqTM II Takara Cat#RR820A Experimental models: Cell lines RAW264.7 RAW264.7 RAW264.7
Article Title: Extracellular vesicles from alveolar macrophages harboring phagocytosed methicillin-resistant Staphylococcus aureus induce necroptosis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-Phospho-RIPK3 Abcam Cat# ab222320; RRID: AB_2868434 Rabbit anti-Phospho-MLKL Abcam Cat# ab196436; RRID: AB_2687465 Rabbit anti-GSDMD Abcam Cat# ab209845; RRID: AB_2783550 Rabbit anti-CD63 Abcam Cat# ab217345; RRID: AB_2754982 Rabbit anti-Caspase1 Abcam Cat# ab179515; RRID: AB_2884954 Rabbit anti-ApoA1 Abcam Cat# ab300085 Rabbit anti-TSG101 ABclonal Cat# A5789; RRID: AB_2863517 Rabbit anti-TRAF6 ABclonal Cat# A16991; RRID: AB_2772697 Rabbit anti-CD9 ABclonal Cat# A1703; RRID: AB_2763755 Rabbit anti-Caspase 7 Abways Cat# CY5579 Rabbit anti-CD81 Affinity Cat# DF2306; RRID: AB_2839530 Rabbit anti-Phospho-RIPK1 Cell Signaling Technology Cat# 53286; RRID: AB_2925183 Rabbit anti-RIPK1 Cell Signaling Technology Cat# 3493; RRID: AB_2305314 Rabbit anti-RIPK3 Cell Signaling Technology Cat# 95702; RRID: AB_2721823 Rabbit anti-MLKL Cell Signaling Technology Cat# 37705; RRID: AB_2799118 Rabbit anti-TNF-a Cell Signaling Technology Cat# 11948; RRID: AB_2687962 Rabbit anti-Caspase3 Cell Signaling Technology Cat# 9662; RRID: AB_331439 Rabbit anti-Caspase8 Cell Signaling Technology Cat# 4790; RRID: AB_10545768 Rabbit anti-Flag Cell Signaling Technology Cat#14793; RRID: AB_2572291 Mouse anti-GAPDH Proteintech Cat# 60004-1-lg; RRID: AB_2919223 Goat anti-mouse lgG Absin Cat# abs20039; RRID: AB_3076309 Goat anti-rabbit lgG Absin Cat# abs20040; RRID: AB_2938713 Anti-mouse F4/80 Biolegend Cat# 123115; RRID: AB_893493 Anti-mouse Siglec-F Biolegend Cat# 155505; RRID: AB_2750235 Anti-mouse CD11b Biolegend Cat# 101212; RRID: AB_312795 Anti-mouse Ly6G Biolegend Cat# 127641; RRID: AB_2565881 Anti-mouse CD63 Biolegend Cat# 143905; RRID: AB_2565495 Rabbit anti-F4/80 Abcam Cat# ab300421; RRID: AB_2936298 Rabbit anti-p-MLKL Cell Signaling Technology Cat# 37333; RRID: AB_2799112 Rabbit anti- Prosurfactant Protein C Abcam Cat# ab211326; RRID: AB_2927746 Purified anti-CD9 Antibody Biolegend Cat# 124802; RRID: AB_1279332 iFluorTM 488 Conjugated goat anti-rabbit lgG Huabio Cat# HA1121 iFluorTM 594 Conjugated goat anti-rabbit lgG Huabio Cat# HA1122 iFluorTM 488 Phalloidin Yeasen Cat# 40736 Bacterial and virus strains USA300 ATCC Cat# BAA-1556 S. aureus ATCC Cat# 25923 Chemicals, peptides, and recombinant proteins DAPI Vector Cat# H-1200 Dynamin IN MedChemExpress Cat# HY-152215 FBS Gibco Cat# 10099158 GW4869 MedChemExpress Cat# HY-19363 INTERFERin Polyplus Transfection Cat# #382 (Continued on next page) Cell Reports 43, 114453, July 23, 2024 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Jetpei Polyplus Transfection Cat# #499 Latex beads Invitrogen Cat# A37304 Nonfat powdered milk Sangon Biotech Cat# A600669-0250 O. C. T Compound SAKURA Cat# 4583 Protease inhibitors Beyotime Cat# P1005 PKH26 Sigma Cat# MID126 Proteinase K MCE Cat# HY-108717 Recombinant mouse TNF-a ABclonal Cat# RP01702 RIPA lysis buffer Beyotime Cat# P0013E Red blood cell lysis buffer Solarbio Cat# R1010 RNase Solarbio Cat# R1030 SYBR Vazyme Cat# Q121-02 TNF-a antagonist MedChemExpress Cat# HY-110203 Type II collagenase Worthington Biochemical Cat# LS004177 RNAiso Plus Takara Cat# 9108 Vancomycin Sangon Biotech Cat# A600983 Critical commercial assays Annexin V-APC/PI Apoptosis Kit Multi Sciences Cat# AT107 CCK-8 Kit Fdbio Cat# FD3788 DABtunel Kit Haokebio Cat# HKI0012 Enhanced Chemiluminescence Substrate Kit NCM Biotech Cat# P10300 Gaussia Luciferase Assay Kit Beyotime Cat# RG021S HiFiScript cDNA Synthesis Kit CWBIO Cat# CW2569 Hairpin-itTM microRNA and U6 snRNA Normalization RT-PCR Quantitation Kit GenePharma Cat# E22001 PierceTM BCA Protein Assay Kit Thermo Fisher Cat# 23225 mmu-IL-1b ELISA Kit Abcam Cat# ab197742 mmu-IL-6 ELISA Kit Abcam Cat# ab222503 mmu-TNF-a ELISA Kit Abcam Cat# ab208348 Deposited data Proteomics data This paper iProX: PXD052452 miRNA-seq data This paper NCBI: PRJNA1113992 Experimental models: Cell lines MH-S cells ATCC ATCC CRL-2019 MLE12 cells ATCC ATCC CRL-2110 Experimental models: Organisms/strains Mouse: C57BL/6J Shanghai SLAC Laboratory Animal Co., Ltd. (Shanghai, China) N/A Oligonucleotides Primers for real-time PCR, see Table S1 This paper N/A miRNA mimics, see Table S1 This paper N/A siRNA, see Table S1 This paper N/A Recombinant DNA TRAF6 plasmid Miaoling Biology P19727 Wild-type pmir-GLO luciferase plasmids of TRAF6 3’ untranslated region GenePharma N/A Mutant pmir-GLO luciferase plasmids of TRAF6 3’ untranslated region GenePharma N/A (Continued on next page) 20 Cell Reports 43, 114453, July 23, 2024
Modification:Article Title: Endogenous IFITMs boost SARS-coronavirus 1 and 2 replication whereas overexpression inhibits infection by relocalizing ACE2.
Article Snippet: .. Antibodies IRDye 680RD Goat anti-Rabbit IgG (H + L) LI-COR Cat926-68071 IRDye 800CW Goat anti-Mouse IgG (H + L) LI-COR Cat# 926-32210 IRDye 800RD Goat anti-Rat IgG (H + L) LI-COR Cat# 925-32219 HCoV-229E Nucleocapsid Antibody SinoBiological Cat# 40640-T62 Anti-Coronavirus NL63 Ingenasa M.30.HCo.I2D4 Anti-Coronavirus Antibody, OC-43 strain Millipore Cat# MAB9012 Purified anti-GAPDH Antibody Biolegend Cat# 607902 Rabbit polyclonal anti-IFITM1 Cell signaling Cat# 13126 S Rabbit polyclonal anti-IFITM2 Cell signaling Cat# 13530S Rabbit polyclonal anti-IFITM3 Cell signaling Cat# 59212S V5-Tag (E9H8O) Mouse mAb Cell signaling Cat# 80076 SARS-CoV-2 (2019-nCoV) Nucleocapsid Antibody SinoBiological Cat# 40588-MM124 Rabbit polyclonal anti-ACE2 Abcam Cat# ab15348 Mouse monoclonal anti-flag Sigma-Aldrich Cat# F1804 Fixable Viability Dye eFluor 780 Thermo Fisher Cat# 65-0865-14 Rabbit monoclonal Alexa Fluor 647 anti-CD46 Abcam Cat# 275208 Rat Monoclonal PerCP-Cy5.5 anti-CD4 Biolegend Cat# 317428 Bacterial and virus strains VSVDG(GFP)*VSV-G Klaus Conzelmann N/A hCoV-229E ATCC Cat# VR-740TM hCoV-NL63 Lia van der Hoek N/A hCoV-OC43 ATCC Cat# CR-1558TM Renilla hCoV-229E Volker Thiel N/A BetaCoV/Netherlands/01/NL/2020 European Virus Archive Cat# 010V 03903 VSVDG(GFP)*VSV-G Klaus Conzelmann N/A BetaCoV/Netherlands/01/NL/2020 European Virus Archive Cat# 010V 03903 BetaCoV/B.1.617.2/Delta Florian Schmidt (University of Bonn) N/A BetaCoV/Munich/BavPat1/2020 GISAID; Wölfel et al., 202047 EPI_ISL_406862 SARS-CoV (rSCV, Frankfurt-1 virus isolate) Pfefferle et al., 200929 Genbank accession no. AY310120 rMERS-CoV, MERS-CoV/EMC2012 Muth et al., 201748 Genbank accession no. NC_019843.3 Chemicals, peptides, and recombinant proteins L-Glutamine Pan Biotech Cat# P04-80100 DAPI Sigma-Aldrich Cat# D9542-1MG; CAS: 28718-90-3 Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat# 41965039 Dulbecco’s Phosphate Buffered Saline (PBS) Thermo Fisher Cat# 14190094 Minimum Essential Medium Eagle (MEM) Sigma-Aldrich Cat# M4655 Opti-MEM Gibco Cat# M3942 Roswell Park Memorial Institute (RPMI) Gibco Cat# 22400089 Penicillin-Streptomycin Thermo Fisher Cat# 15140122 non-essential amino acids Sigma-Aldrich Cat# M7145 (Continued on next page) iScience 26, 106395, April 21, 2023 17 .. Sodium pyruvate Sigma-Aldrich Cat# S8636 FCS Gibco Cat# 10270106 Trypsin EDTA Gibco Cat# T3924 Versene Thermo Fisher Cat# 15040066 TMB peroxidase substrate (Sure blue) Medac Cat# 52-00-04 BD Cytofix/Cytoperm Fixation/Permeabilization Solution Kit BD Biosciences Cat# 554714 Lipofectamine RNAiMAX ThermoFisher Cat# 13778075 SuperScript III Platinum One-Step qRT-PCR Kit Invitrogen Cat# 11732088 Renilla Luciferase Assay kit Promega Cat# E2810 Quick RNA Miniprep Kit ZYMO research Cat# R1055 QIAamp Viral RNA Kits QIAGEN Cat# 52906 Luciferase Assay Kit Promega Cat# E1500 Mowiol 4-88 ROTH Cat# 0713.1 Blocker Casein in PBS Thermo Fisher Cat# 37528 TaqMan Fast Virus 1-Step Master Mix ThermoFisher Cat# 4444436 Tween 20 Sigma-Aldrich Cat# P7949500ML Triton X-100 Sigma-Aldrich Cat#T9284 100ML GAPD (GAPDH) Endogenous Control ThermoFisher Cat# 4352338E b-Mercaptoethanol Sigma-Aldrich Cat# 444203 Immobilon-FL PVDF membranes Merck Millipore Cat# IPVH00010 Paraformaldehyde Merck, Darmstadt Cat# 104005 TransIT-LT1 Mirus Cat# MIR2300 NuPAGE 4G12% Bis-Tris Gels ThermoFisher Cat# NP0321BOX Synthetic SARS-CoV-2-RNA Twist Bioscience Cat# 102019 RNAiMAX ThermoFisher Cat# LMRNA015 Recombinant IFN-a2 pbl assay science Cat# 11101-1 Recombinant IFN-b R&D systems Cat# 8499-IF-010 Recombinant IFN-g Sigma-Aldrich Cat# I3265 Recombinant IFN- l3 CHO Cat# 5259-IL-025 Cytochalasin D ThermoFisher Cat# PHZ1063 Agarose Sigma-Aldrich Cat# A9539 Experimental models: Cell lines Human: Calu-3 ATCC or M. Frick Cat# HTB-55 or N/A Human: Caco2 Holger Barth Human: Huh7.5 Ralf Bartenschlager Human: Huh7 Anna-Laura Kretz LLCMK2 by Lia van der Hoek
Article Title: Vimentin inhibits type I interferon production by disrupting the TBK1-IKKε-IRF3 axis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-Flag-Rabbit SIGMA Cat#F7425-2MG; RRID: AB-2572291 anti-LaminB-Rabbit Solarbio Cat# K106482P- anti-HSV-1 Abcam Cat# ab6506 anti-IFNAR1-Rabbit Abcam Cat# ab124764 anti-Flag-Mouse SIGMA Cat# F1804-1MG anti-HA-Rabbit SIGMA Cat# SAB4300603 anti-HA-Mouse SIGMA Cat# HS658-2ML anti-GFP-Rabbit Proteintech Cat# 50430-2-AP anti-Vimentin-Rabbit Cell Signaling Technology Cat# 5741S anti-Vimentin-Mouse Abcam Cat#ab20346 anti-IRF3 Cell Signaling Technology Cat#4302; RRID: AB-1904036 anti-IRF3 phosphorylated at S396 Cell Signaling Technology Cat#4947; RRID: AB-823547 anti-TBK1 Cell Signaling Technology Cat#3504; RRID: AB-2255663 anti-TBK1 phosphorylated at S172 Cell Signaling Technology Cat#5483 anti-GAPDH Proteintech Group Cat#60004-1-Ig; RRID: AB-2107436 Anti-IKKε RD systems Cat#MAB3199 Alexa Flour 488 goat anti-rabbit IgG(H + L) Invitrogen Cat#A11008 Alexa Flour 633 goat anti-rabbit IgG(H + L) Invitrogen Cat#A21071 Alexa Flour 633 goat anti-mouse IgG(H + L) Invitrogen Cat#A21052 Alexa Flour 594 goat anti-mouse IgG(H + L) Invitrogen Cat#A11032 IRDye 800CW Goat anti-rabbit IgG (H + L) LI-COR Cat#926-32211 IRDye 800CW Goat anti-mouse IgG (H + L) LI-COR Cat#926-32210 Bacterial and virus strains The Sendai/Cantell strain ATCC ATCC VR-907 VSV-GFP Harbin Veterinary Research Institute N/A VSV-GFP Harbin Veterinary Research Institute N/A HSV-1-GFP Harbin Veterinary Research Institute N/A EMCV (HB10); GeneBank: JQ864080.1 Isolated from Pig N/A ADV Hanbio Biotechnology Co., Ltd. N/A Chemicals, peptides, and recombinant proteins anti-Flag (M2) beads Sigma-Aldrich Cat#M8823 Protein agarose A/G Santa Cruz Biotechnology Cat#20397 TRIzol reagent Invitrogen Cat#15596026 Poly(I:C) Sigma-Aldrich Cat#P1530 cGAMP Sigma-Aldrich Cat#SML1232-1EA Poly (dA:dT) Sigma-Aldrich Cat#P0883-10UN ISD Invitrogen Cat#tlrl-isdn protease inhibitor Cocktail Roche Cat#4693132001 Dulbecco’s Modified Eagle’s Medium (DMEM) GIBCO Cat#C11995500CP RPMI 1640 medium GIBCO Cat#C11875500CP fetal bovine serum (FBS) GIBCO Cat#10091-148 (Continued on next page) e1 Cell Reports 41, 111469, October 11, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Penicillin-Streptomycin Solution Hyclone Cat#SV30010 thioglycollate MERCK Cat#1.08191 Critical commercial assays Dual-Luciferase Reporter Assay System Promega Cat#E1910 PrimeScriptTM RT Reagent Kit Takara Cat# RR037A SYBR Premix Ex TaqTM II Takara Cat#RR820A Experimental models: Cell lines RAW264.7 RAW264.7 RAW264.7
Saline:Article Title: Endogenous IFITMs boost SARS-coronavirus 1 and 2 replication whereas overexpression inhibits infection by relocalizing ACE2.
Article Snippet: .. Antibodies IRDye 680RD Goat anti-Rabbit IgG (H + L) LI-COR Cat926-68071 IRDye 800CW Goat anti-Mouse IgG (H + L) LI-COR Cat# 926-32210 IRDye 800RD Goat anti-Rat IgG (H + L) LI-COR Cat# 925-32219 HCoV-229E Nucleocapsid Antibody SinoBiological Cat# 40640-T62 Anti-Coronavirus NL63 Ingenasa M.30.HCo.I2D4 Anti-Coronavirus Antibody, OC-43 strain Millipore Cat# MAB9012 Purified anti-GAPDH Antibody Biolegend Cat# 607902 Rabbit polyclonal anti-IFITM1 Cell signaling Cat# 13126 S Rabbit polyclonal anti-IFITM2 Cell signaling Cat# 13530S Rabbit polyclonal anti-IFITM3 Cell signaling Cat# 59212S V5-Tag (E9H8O) Mouse mAb Cell signaling Cat# 80076 SARS-CoV-2 (2019-nCoV) Nucleocapsid Antibody SinoBiological Cat# 40588-MM124 Rabbit polyclonal anti-ACE2 Abcam Cat# ab15348 Mouse monoclonal anti-flag Sigma-Aldrich Cat# F1804 Fixable Viability Dye eFluor 780 Thermo Fisher Cat# 65-0865-14 Rabbit monoclonal Alexa Fluor 647 anti-CD46 Abcam Cat# 275208 Rat Monoclonal PerCP-Cy5.5 anti-CD4 Biolegend Cat# 317428 Bacterial and virus strains VSVDG(GFP)*VSV-G Klaus Conzelmann N/A hCoV-229E ATCC Cat# VR-740TM hCoV-NL63 Lia van der Hoek N/A hCoV-OC43 ATCC Cat# CR-1558TM Renilla hCoV-229E Volker Thiel N/A BetaCoV/Netherlands/01/NL/2020 European Virus Archive Cat# 010V 03903 VSVDG(GFP)*VSV-G Klaus Conzelmann N/A BetaCoV/Netherlands/01/NL/2020 European Virus Archive Cat# 010V 03903 BetaCoV/B.1.617.2/Delta Florian Schmidt (University of Bonn) N/A BetaCoV/Munich/BavPat1/2020 GISAID; Wölfel et al., 202047 EPI_ISL_406862 SARS-CoV (rSCV, Frankfurt-1 virus isolate) Pfefferle et al., 200929 Genbank accession no. AY310120 rMERS-CoV, MERS-CoV/EMC2012 Muth et al., 201748 Genbank accession no. NC_019843.3 Chemicals, peptides, and recombinant proteins L-Glutamine Pan Biotech Cat# P04-80100 DAPI Sigma-Aldrich Cat# D9542-1MG; CAS: 28718-90-3 Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat# 41965039 Dulbecco’s Phosphate Buffered Saline (PBS) Thermo Fisher Cat# 14190094 Minimum Essential Medium Eagle (MEM) Sigma-Aldrich Cat# M4655 Opti-MEM Gibco Cat# M3942 Roswell Park Memorial Institute (RPMI) Gibco Cat# 22400089 Penicillin-Streptomycin Thermo Fisher Cat# 15140122 non-essential amino acids Sigma-Aldrich Cat# M7145 (Continued on next page) iScience 26, 106395, April 21, 2023 17 .. Sodium pyruvate Sigma-Aldrich Cat# S8636 FCS Gibco Cat# 10270106 Trypsin EDTA Gibco Cat# T3924 Versene Thermo Fisher Cat# 15040066 TMB peroxidase substrate (Sure blue) Medac Cat# 52-00-04 BD Cytofix/Cytoperm Fixation/Permeabilization Solution Kit BD Biosciences Cat# 554714 Lipofectamine RNAiMAX ThermoFisher Cat# 13778075 SuperScript III Platinum One-Step qRT-PCR Kit Invitrogen Cat# 11732088 Renilla Luciferase Assay kit Promega Cat# E2810 Quick RNA Miniprep Kit ZYMO research Cat# R1055 QIAamp Viral RNA Kits QIAGEN Cat# 52906 Luciferase Assay Kit Promega Cat# E1500 Mowiol 4-88 ROTH Cat# 0713.1 Blocker Casein in PBS Thermo Fisher Cat# 37528 TaqMan Fast Virus 1-Step Master Mix ThermoFisher Cat# 4444436 Tween 20 Sigma-Aldrich Cat# P7949500ML Triton X-100 Sigma-Aldrich Cat#T9284 100ML GAPD (GAPDH) Endogenous Control ThermoFisher Cat# 4352338E b-Mercaptoethanol Sigma-Aldrich Cat# 444203 Immobilon-FL PVDF membranes Merck Millipore Cat# IPVH00010 Paraformaldehyde Merck, Darmstadt Cat# 104005 TransIT-LT1 Mirus Cat# MIR2300 NuPAGE 4G12% Bis-Tris Gels ThermoFisher Cat# NP0321BOX Synthetic SARS-CoV-2-RNA Twist Bioscience Cat# 102019 RNAiMAX ThermoFisher Cat# LMRNA015 Recombinant IFN-a2 pbl assay science Cat# 11101-1 Recombinant IFN-b R&D systems Cat# 8499-IF-010 Recombinant IFN-g Sigma-Aldrich Cat# I3265 Recombinant IFN- l3 CHO Cat# 5259-IL-025 Cytochalasin D ThermoFisher Cat# PHZ1063 Agarose Sigma-Aldrich Cat# A9539 Experimental models: Cell lines Human: Calu-3 ATCC or M. Frick Cat# HTB-55 or N/A Human: Caco2 Holger Barth Human: Huh7.5 Ralf Bartenschlager Human: Huh7 Anna-Laura Kretz LLCMK2 by Lia van der Hoek
Isolation:Article Title: Vimentin inhibits type I interferon production by disrupting the TBK1-IKKε-IRF3 axis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-Flag-Rabbit SIGMA Cat#F7425-2MG; RRID: AB-2572291 anti-LaminB-Rabbit Solarbio Cat# K106482P- anti-HSV-1 Abcam Cat# ab6506 anti-IFNAR1-Rabbit Abcam Cat# ab124764 anti-Flag-Mouse SIGMA Cat# F1804-1MG anti-HA-Rabbit SIGMA Cat# SAB4300603 anti-HA-Mouse SIGMA Cat# HS658-2ML anti-GFP-Rabbit Proteintech Cat# 50430-2-AP anti-Vimentin-Rabbit Cell Signaling Technology Cat# 5741S anti-Vimentin-Mouse Abcam Cat#ab20346 anti-IRF3 Cell Signaling Technology Cat#4302; RRID: AB-1904036 anti-IRF3 phosphorylated at S396 Cell Signaling Technology Cat#4947; RRID: AB-823547 anti-TBK1 Cell Signaling Technology Cat#3504; RRID: AB-2255663 anti-TBK1 phosphorylated at S172 Cell Signaling Technology Cat#5483 anti-GAPDH Proteintech Group Cat#60004-1-Ig; RRID: AB-2107436 Anti-IKKε RD systems Cat#MAB3199 Alexa Flour 488 goat anti-rabbit IgG(H + L) Invitrogen Cat#A11008 Alexa Flour 633 goat anti-rabbit IgG(H + L) Invitrogen Cat#A21071 Alexa Flour 633 goat anti-mouse IgG(H + L) Invitrogen Cat#A21052 Alexa Flour 594 goat anti-mouse IgG(H + L) Invitrogen Cat#A11032 IRDye 800CW Goat anti-rabbit IgG (H + L) LI-COR Cat#926-32211 IRDye 800CW Goat anti-mouse IgG (H + L) LI-COR Cat#926-32210 Bacterial and virus strains The Sendai/Cantell strain ATCC ATCC VR-907 VSV-GFP Harbin Veterinary Research Institute N/A VSV-GFP Harbin Veterinary Research Institute N/A HSV-1-GFP Harbin Veterinary Research Institute N/A EMCV (HB10); GeneBank: JQ864080.1 Isolated from Pig N/A ADV Hanbio Biotechnology Co., Ltd. N/A Chemicals, peptides, and recombinant proteins anti-Flag (M2) beads Sigma-Aldrich Cat#M8823 Protein agarose A/G Santa Cruz Biotechnology Cat#20397 TRIzol reagent Invitrogen Cat#15596026 Poly(I:C) Sigma-Aldrich Cat#P1530 cGAMP Sigma-Aldrich Cat#SML1232-1EA Poly (dA:dT) Sigma-Aldrich Cat#P0883-10UN ISD Invitrogen Cat#tlrl-isdn protease inhibitor Cocktail Roche Cat#4693132001 Dulbecco’s Modified Eagle’s Medium (DMEM) GIBCO Cat#C11995500CP RPMI 1640 medium GIBCO Cat#C11875500CP fetal bovine serum (FBS) GIBCO Cat#10091-148 (Continued on next page) e1 Cell Reports 41, 111469, October 11, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Penicillin-Streptomycin Solution Hyclone Cat#SV30010 thioglycollate MERCK Cat#1.08191 Critical commercial assays Dual-Luciferase Reporter Assay System Promega Cat#E1910 PrimeScriptTM RT Reagent Kit Takara Cat# RR037A SYBR Premix Ex TaqTM II Takara Cat#RR820A Experimental models: Cell lines RAW264.7 RAW264.7 RAW264.7
Protease Inhibitor:Article Title: Vimentin inhibits type I interferon production by disrupting the TBK1-IKKε-IRF3 axis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-Flag-Rabbit SIGMA Cat#F7425-2MG; RRID: AB-2572291 anti-LaminB-Rabbit Solarbio Cat# K106482P- anti-HSV-1 Abcam Cat# ab6506 anti-IFNAR1-Rabbit Abcam Cat# ab124764 anti-Flag-Mouse SIGMA Cat# F1804-1MG anti-HA-Rabbit SIGMA Cat# SAB4300603 anti-HA-Mouse SIGMA Cat# HS658-2ML anti-GFP-Rabbit Proteintech Cat# 50430-2-AP anti-Vimentin-Rabbit Cell Signaling Technology Cat# 5741S anti-Vimentin-Mouse Abcam Cat#ab20346 anti-IRF3 Cell Signaling Technology Cat#4302; RRID: AB-1904036 anti-IRF3 phosphorylated at S396 Cell Signaling Technology Cat#4947; RRID: AB-823547 anti-TBK1 Cell Signaling Technology Cat#3504; RRID: AB-2255663 anti-TBK1 phosphorylated at S172 Cell Signaling Technology Cat#5483 anti-GAPDH Proteintech Group Cat#60004-1-Ig; RRID: AB-2107436 Anti-IKKε RD systems Cat#MAB3199 Alexa Flour 488 goat anti-rabbit IgG(H + L) Invitrogen Cat#A11008 Alexa Flour 633 goat anti-rabbit IgG(H + L) Invitrogen Cat#A21071 Alexa Flour 633 goat anti-mouse IgG(H + L) Invitrogen Cat#A21052 Alexa Flour 594 goat anti-mouse IgG(H + L) Invitrogen Cat#A11032 IRDye 800CW Goat anti-rabbit IgG (H + L) LI-COR Cat#926-32211 IRDye 800CW Goat anti-mouse IgG (H + L) LI-COR Cat#926-32210 Bacterial and virus strains The Sendai/Cantell strain ATCC ATCC VR-907 VSV-GFP Harbin Veterinary Research Institute N/A VSV-GFP Harbin Veterinary Research Institute N/A HSV-1-GFP Harbin Veterinary Research Institute N/A EMCV (HB10); GeneBank: JQ864080.1 Isolated from Pig N/A ADV Hanbio Biotechnology Co., Ltd. N/A Chemicals, peptides, and recombinant proteins anti-Flag (M2) beads Sigma-Aldrich Cat#M8823 Protein agarose A/G Santa Cruz Biotechnology Cat#20397 TRIzol reagent Invitrogen Cat#15596026 Poly(I:C) Sigma-Aldrich Cat#P1530 cGAMP Sigma-Aldrich Cat#SML1232-1EA Poly (dA:dT) Sigma-Aldrich Cat#P0883-10UN ISD Invitrogen Cat#tlrl-isdn protease inhibitor Cocktail Roche Cat#4693132001 Dulbecco’s Modified Eagle’s Medium (DMEM) GIBCO Cat#C11995500CP RPMI 1640 medium GIBCO Cat#C11875500CP fetal bovine serum (FBS) GIBCO Cat#10091-148 (Continued on next page) e1 Cell Reports 41, 111469, October 11, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Penicillin-Streptomycin Solution Hyclone Cat#SV30010 thioglycollate MERCK Cat#1.08191 Critical commercial assays Dual-Luciferase Reporter Assay System Promega Cat#E1910 PrimeScriptTM RT Reagent Kit Takara Cat# RR037A SYBR Premix Ex TaqTM II Takara Cat#RR820A Experimental models: Cell lines RAW264.7 RAW264.7 RAW264.7
In Vitro:
Incubation:Article Title: Effective Search of Triterpenes with Anti-HSV-1 Activity Using a Classification Model by Logistic Regression
Article Snippet: .. The anti-HSV-1 assay conditions for these data included incubation times of 12–48 h and cell types of HeLa cells, Vero cells, and virus strains of mainly KOS (ATCC ® VR1493), Strain F (ATCC ® VR-733), and 17 (GenBank acc. no. NC_001,806) and HSV-1 MI (ATCC ® VR-539), which were acyclovir-sensitive strain. .. With the threshold of activity set to 25 μ M, 166 active and 250 inactive compounds were defined ( ); shows the results of the PCA of active or inactive compounds collected from ChEMBL, DNP, and the original papers using 267 descriptors.
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