Virus:Article Title: Generation of antigen-specific paired-chain antibodies using large language models.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Goat anti-human IgG-HRP Thermo Fisher Cat # A18817; RRID: AB_2535594 Mouse anti-RSV F (MCA490) Bio-Rad Cat# MCA490; RRID:AB_2231368 S309 PMID: 32422645 PBD: 6WS6 VRC01 BEI Resources ARP-12033; RRID: AB_2491019 CR9114 PMID: 22878502 GenBank: JX213639, JX213640 MEDI8852 PMID: 27453466 RRID: AB_3111586 5-1 Abu-Shmais et al. 35 N/A APC-Cy7 Mouse Anti-Human CD14 BD Cat# 561709; RRID: AB_10893806 FITC Anti-Human CD3 (OKT3) Tonbo Biosciences Cat# 35–0037; RRID: AB_2621662 BV711 Mouse Anti-Human CD19 BD Cat# 563036; RRID: AB_2737968 PE-Cy5 Mouse Anti-Human IgG BD Cat# 551497; RRID: AB_394220 Bacterial and virus strains RSV A2 strain BEI Resources NR-52018 SARS-CoV-2 index pseudovirus Daniel Sheward N/A SARS-CoV-1 pseudovirus Daniel Sheward N/A SARS-CoV-2 Delta pseudotyped lentivirus Daniel Sheward N/A SARS-CoV-2 Gamma pseudotyped lentivirus Daniel Sheward N/A SARS-CoV-2 BA.2.75.2 pseudotyped lentivirus Daniel Sheward N/A SARS-CoV-2 B.1 pseudotyped lentivirus Daniel Sheward N/A SARS-CoV-2 BJ.1 pseudotyped lentivirus Daniel Sheward N/A SARS-CoV-2 BA.2 pseudotyped lentivirus Daniel Sheward N/A SARS-CoV-2 BA.5 pseudotyped lentivirus Daniel Sheward N/A SARS-CoV-2 BQ.1.1 pseudotyped lentivirus Daniel Sheward N/A SARS-CoV-2 JN.1 pseudotyped lentivirus Daniel Sheward N/A SARS-CoV-2 XBB.1.5 pseudotyped lentivirus Daniel Sheward N/A H5N1 A/Texas/37/2024 Rebecca A. Gillespie N/A H5N1 A/Vietnam/1203/2004 Rebecca A. Gillespie N/A H1N1 A/Michigan/45/2015 Rebecca A. Gillespie N/A H5N1 A/Cambodia/2023 Rebecca A. Gillespie N/A H5N2 A/Mexico/2024 Rebecca A. Gillespie N/A H2N2 A/Singapore/1/57 Rebecca A. Gillespie N/A Biological samples Human PBMCs (healthy) StemCell Technologies Cat# 70025 Human PBMCs (HIV-1+) Mark Connors N/A Human PBMCs (COVID-19 convalescent) Helen Chu N/A Human PBMCs (Influenza vaccinated) Ted Ross N/A Chemicals, peptides, and recombinant proteins Polyethyleniminine Linear MW 25000 Polysciences Cat#23966-1 1-Step Ultra TMB-ELISA Substrate Solution Thermo Fisher Cat#34029 Pluronic Acid F-68 Fisher Cat# 24040-032 Bovine serum albumin (BSA) Sigma-Aldrich A1470 Ghost dye red 780 Tonbo biosciences Cat#13-0865 4 mM L-glutamine Fisher Cat# 25030-081 Protein A resin GenScript Cat#L00210 (Continued on next page) ll OPEN ACCESS Cell 188, 1–16.e1–e8, December 11, 2025 e1 Please cite this article in press as: Wasdin et al., Generation of antigen-specific paired-chain antibodies using large language models, Cell (2025), https://doi.org/10.1016/j.cell.2025.10.006 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Lyra-CoV Spike Wall et al. 31 N/A SARS-CoV-2 Index RBD Sino Biological Cat# 40592-VNAH SARS-CoV-2 HexaPro Index Spike PMID: 32703906 N/A SARS-CoV-1 S Jason McLellan N/A HCoV-OC43 S Jason McLellan N/A HCoV-HKU1-S-2P PMID: 28807998 N/A RSV A2 DS-Cav1 prefusion F Jason McLellan N/A RSV B9320 DS-Cav1 prefusion F Jason McLellan N/A RSV post-fusion Jason McLellan N/A hMPV F A1(NL/1/00) Jason McLellan N/A hMPV F B2(TN99-419) Jason McLellan N/A hMPV A postfusion F Jason McLellan N/A Parainfluenza virus type 3 prefusion stabilized F ectodomain PMID: 30420505 PDB: 6MJZ H5/TX/24 hemagglutinin Genscript GenBank PP577943.1 H3 HK68 Masaru Kanekiyo N/A H3 Perth19 Masaru Kanekiyo N/A H1 MI15 Masaru Kanekiyo N/A H1 NC99 Masaru Kanekiyo N/A B2 SG57 Masaru Kanekiyo N/A HA B/Wash/19 Masaru Kanekiyo N/A H5 VN04 Masaru Kanekiyo N/A H5 IN05 Masaru Kanekiyo N/A H7 Anh13 Masaru Kanekiyo N/A H5 HK09 Masaru Kanekiyo N/A H10 JD13 Masaru Kanekiyo N/A HIV-1 gp140 SOSIP BG505 Ivelin Georgiev N/A HIV-1 ZM197 env Ivelin Georgiev N/A HIV-1 B4.1 env Ivelin Georgiev N/A Norovirus CHDC P domain Grant Hansman N/A Norovirus SYD_2012 P domain Grant Hansman N/A Norovirus GII.17 P domain Grant Hansman N/A Critical commercial assays B cell Single Cell V(D)J solution 10X Genomics N/A ExpiFectamineTM 293 Transfection Kit Thermo Fisher Cat #A14526 EZ-link Sulfo-NHS-Biotin No-Weigh Thermo Fisher Cat #A39258 Solulink protein-oligonucleotide conjugation kit TriLink Biotechnologies Cat#S-9011 Plasmid Kits for Plasmid DNA Extraction QIAGEN Cat#12165 StrepTrap XT prepacked chromatography column Cytiva Cat#29401322 Deposited data Raw next-generation sequencing data This paper SRA: PRJNA1321287 Cryo-EM structure RSV-3301 and RSV-2245 fabs bound to RSV-A F This paper PDB: 9MKN, EMDB: EMD-48331 Experimental models: Cell lines Human: Expi293F cells Thermo Fisher Cat#A14527 HEK293T ATCC CRL-3216 Vero cells ATCC CCL-81 E. coli DH5α Cell Culture Core N/A (Continued on next page) ll OPEN ACCESS e2 Cell 188, 1–16.e1–e8, December 11, 2025 Please cite this article in press as: Wasdin et al., Generation of antigen-specific paired-chain antibodies using large language models, Cell (2025), https://doi.org/10.1016/j.cell.2025.10.006 Article
Recombinant:Article Title: Generation of antigen-specific paired-chain antibodies using large language models.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Goat anti-human IgG-HRP Thermo Fisher Cat # A18817; RRID: AB_2535594 Mouse anti-RSV F (MCA490) Bio-Rad Cat# MCA490; RRID:AB_2231368 S309 PMID: 32422645 PBD: 6WS6 VRC01 BEI Resources ARP-12033; RRID: AB_2491019 CR9114 PMID: 22878502 GenBank: JX213639, JX213640 MEDI8852 PMID: 27453466 RRID: AB_3111586 5-1 Abu-Shmais et al. 35 N/A APC-Cy7 Mouse Anti-Human CD14 BD Cat# 561709; RRID: AB_10893806 FITC Anti-Human CD3 (OKT3) Tonbo Biosciences Cat# 35–0037; RRID: AB_2621662 BV711 Mouse Anti-Human CD19 BD Cat# 563036; RRID: AB_2737968 PE-Cy5 Mouse Anti-Human IgG BD Cat# 551497; RRID: AB_394220 Bacterial and virus strains RSV A2 strain BEI Resources NR-52018 SARS-CoV-2 index pseudovirus Daniel Sheward N/A SARS-CoV-1 pseudovirus Daniel Sheward N/A SARS-CoV-2 Delta pseudotyped lentivirus Daniel Sheward N/A SARS-CoV-2 Gamma pseudotyped lentivirus Daniel Sheward N/A SARS-CoV-2 BA.2.75.2 pseudotyped lentivirus Daniel Sheward N/A SARS-CoV-2 B.1 pseudotyped lentivirus Daniel Sheward N/A SARS-CoV-2 BJ.1 pseudotyped lentivirus Daniel Sheward N/A SARS-CoV-2 BA.2 pseudotyped lentivirus Daniel Sheward N/A SARS-CoV-2 BA.5 pseudotyped lentivirus Daniel Sheward N/A SARS-CoV-2 BQ.1.1 pseudotyped lentivirus Daniel Sheward N/A SARS-CoV-2 JN.1 pseudotyped lentivirus Daniel Sheward N/A SARS-CoV-2 XBB.1.5 pseudotyped lentivirus Daniel Sheward N/A H5N1 A/Texas/37/2024 Rebecca A. Gillespie N/A H5N1 A/Vietnam/1203/2004 Rebecca A. Gillespie N/A H1N1 A/Michigan/45/2015 Rebecca A. Gillespie N/A H5N1 A/Cambodia/2023 Rebecca A. Gillespie N/A H5N2 A/Mexico/2024 Rebecca A. Gillespie N/A H2N2 A/Singapore/1/57 Rebecca A. Gillespie N/A Biological samples Human PBMCs (healthy) StemCell Technologies Cat# 70025 Human PBMCs (HIV-1+) Mark Connors N/A Human PBMCs (COVID-19 convalescent) Helen Chu N/A Human PBMCs (Influenza vaccinated) Ted Ross N/A Chemicals, peptides, and recombinant proteins Polyethyleniminine Linear MW 25000 Polysciences Cat#23966-1 1-Step Ultra TMB-ELISA Substrate Solution Thermo Fisher Cat#34029 Pluronic Acid F-68 Fisher Cat# 24040-032 Bovine serum albumin (BSA) Sigma-Aldrich A1470 Ghost dye red 780 Tonbo biosciences Cat#13-0865 4 mM L-glutamine Fisher Cat# 25030-081 Protein A resin GenScript Cat#L00210 (Continued on next page) ll OPEN ACCESS Cell 188, 1–16.e1–e8, December 11, 2025 e1 Please cite this article in press as: Wasdin et al., Generation of antigen-specific paired-chain antibodies using large language models, Cell (2025), https://doi.org/10.1016/j.cell.2025.10.006 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Lyra-CoV Spike Wall et al. 31 N/A SARS-CoV-2 Index RBD Sino Biological Cat# 40592-VNAH SARS-CoV-2 HexaPro Index Spike PMID: 32703906 N/A SARS-CoV-1 S Jason McLellan N/A HCoV-OC43 S Jason McLellan N/A HCoV-HKU1-S-2P PMID: 28807998 N/A RSV A2 DS-Cav1 prefusion F Jason McLellan N/A RSV B9320 DS-Cav1 prefusion F Jason McLellan N/A RSV post-fusion Jason McLellan N/A hMPV F A1(NL/1/00) Jason McLellan N/A hMPV F B2(TN99-419) Jason McLellan N/A hMPV A postfusion F Jason McLellan N/A Parainfluenza virus type 3 prefusion stabilized F ectodomain PMID: 30420505 PDB: 6MJZ H5/TX/24 hemagglutinin Genscript GenBank PP577943.1 H3 HK68 Masaru Kanekiyo N/A H3 Perth19 Masaru Kanekiyo N/A H1 MI15 Masaru Kanekiyo N/A H1 NC99 Masaru Kanekiyo N/A B2 SG57 Masaru Kanekiyo N/A HA B/Wash/19 Masaru Kanekiyo N/A H5 VN04 Masaru Kanekiyo N/A H5 IN05 Masaru Kanekiyo N/A H7 Anh13 Masaru Kanekiyo N/A H5 HK09 Masaru Kanekiyo N/A H10 JD13 Masaru Kanekiyo N/A HIV-1 gp140 SOSIP BG505 Ivelin Georgiev N/A HIV-1 ZM197 env Ivelin Georgiev N/A HIV-1 B4.1 env Ivelin Georgiev N/A Norovirus CHDC P domain Grant Hansman N/A Norovirus SYD_2012 P domain Grant Hansman N/A Norovirus GII.17 P domain Grant Hansman N/A Critical commercial assays B cell Single Cell V(D)J solution 10X Genomics N/A ExpiFectamineTM 293 Transfection Kit Thermo Fisher Cat #A14526 EZ-link Sulfo-NHS-Biotin No-Weigh Thermo Fisher Cat #A39258 Solulink protein-oligonucleotide conjugation kit TriLink Biotechnologies Cat#S-9011 Plasmid Kits for Plasmid DNA Extraction QIAGEN Cat#12165 StrepTrap XT prepacked chromatography column Cytiva Cat#29401322 Deposited data Raw next-generation sequencing data This paper SRA: PRJNA1321287 Cryo-EM structure RSV-3301 and RSV-2245 fabs bound to RSV-A F This paper PDB: 9MKN, EMDB: EMD-48331 Experimental models: Cell lines Human: Expi293F cells Thermo Fisher Cat#A14527 HEK293T ATCC CRL-3216 Vero cells ATCC CCL-81 E. coli DH5α Cell Culture Core N/A (Continued on next page) ll OPEN ACCESS e2 Cell 188, 1–16.e1–e8, December 11, 2025 Please cite this article in press as: Wasdin et al., Generation of antigen-specific paired-chain antibodies using large language models, Cell (2025), https://doi.org/10.1016/j.cell.2025.10.006 Article
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