| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-HLA class I-FITC (W6/32) | BioLegend | AB_314873 |
| anti-HLA-E-PE (3D12) | BioLegend | AB_1659249 |
| anti-HLA-E (3D12) | ThermoFisher | AB_1210774 |
| anti-CD14-V500 (M5E2) | BD Biosciences | AB_10611856 |
| anti-CD19-BV570 (HIB19) | BioLegend | AB_2563606 |
| anti-CD3-PE-Cy5 (UCHT1) | Beckman Coulter | AB_2827419 |
| anti-CD56-BUV737 (NCAM16.2) | BD Biosciences | AB_2860005 |
| anti-CD56-ECD (N901) | Beckman Coulter | AB_2750853 |
| anti-CD16-BV786 (3G8) | BioLegend | AB_2563803 |
| anti-CD57-PacificBlue (HCD57) | BioLegend | AB_2063198 |
| anti-NKG2A-ViobrightFITC (REA110) | Miltenyi Biotec | AB_2726173 |
| anti-NKG2C-PE (REA205) | Miltenyi Biotec | AB_2751835 |
| anti-KIR2DL1-APC (REA284) | Miltenyi Biotec | AB_2752101 |
| anti-KIR2DL3-Biotin (REA147) | Miltenyi Biotec | AB_2655344 |
| anti-KIR3DL1-APC-Fire750 (DX9) | BioLegend | AB_2687394 |
| anti-KIR2DL1/DS1-PE-Cy7 (EB6) | Beckman Coulter | AB_2801261 |
| anti-KIR2DL2/L3/S2-PE-Cy5.5 (GL183) | Beckman Coulter | AB_2857331 |
| anti-CD107a-BUV395 (H3A4) | BD Biosciences | AB_2739073 |
| anti-TNF-BV650 (MAb11) | BioLegend | AB_2562741 |
| anti-IFN-γ-Alexa700 (B27) | BD Biosciences | AB_396977 |
| anti-CD94 (#131412) | R&D Systems | AB_2234380 |
| Bacterial and virus strains | ||
| SARS-CoV-2/human/SWE/01/2020 | Public Health Agency of Sweden | MT093571.1 |
| Biological samples | ||
| Buffy coats from healthy donors | Department of Clinical Immunology and Transfusion Medicine, Karolinska Institute | N/A |
| Cohort of patients with COVID-19 and healthy controls | Maucourant et al. 2020; Table S1 | https://covid19cellatlas.com/ |
| Chemicals, peptides, and recombinant proteins | ||
| pp65495-503 (NLVPMVATV) | Peptides&Elephants | EP04509_1 |
| HLA-C3-11 (VMAPRTLIL) | Peptides&Elephants | EP06244_1 |
| Nsp13232-240 (VMPLSAPTL) | Peptides&Elephants | N/A |
| S269-277 (YLQPRTFLL) | Peptides&Elephants | N/A |
| Nsp6114-122 (VMYASAVVL) | Peptides&Elephants | N/A |
| Biotinylated Human NKG2A&CD94 Protein | Acro Biosystems | NC4-H82F5 |
| Gibco Human IL-15 Recombinant Protein | ThermoFisher | PHC9151 |
| Recombinant Human IFN-Alpha2a | PBL Assay Science | 11101-2 |
| Critical commercial assays | ||
| BD Cytofix/Cytoperm™ | BD Biosciences | AB_2869008 |
| RNeasy Micro Plus Kit | Qiagen | 74034 |
| SARS-CoV-2 (2019-nCoV) CDC qPCR Probe Assay, RUO Kit | IDT | 10006713 |
| TaqPath™ 1-Step RT-qPCR Master Mix, CG | ThermoFisher | A15299 |
| Deposited data | ||
| HCMV pp65 protein sequence | UniProt | P06725 |
| HLA-C∗01:02:01:01 protein sequence | IMGT | HLA00401 |
| SARS-CoV-2 isolate Wuhan-Hu-1 genomic sequence | GenBank | NC_045512.2 |
| Human CD94/NKG2A in complex with HLA-E crystal structure | PDB | 3CDG |
| SARS coronavirus Tor2 genomic sequence | GenBank | NC_004718.3 |
| Human coronavirus HKU1 genomic sequence | GenBank | NC_006577.2 |
| Human coronavirus OC43 genomic sequence | GenBank | AY391777.1 |
| Human coronavirus NL63 genomic sequence | GenBank | NC_005831.2 |
| Human coronavirus 229E genomic sequence | GenBank | NC_002645.1 |
| Bat SARS-like coronavirus isolate Rf4092 genomic sequence | GenBank | KY417145.1 |
| Bat coronavirus Cp/Yunnan2011 genomic sequence | GenBank | JX993988.1 |
| Bat SARS-like coronavirus isolate Rs4084 genomic sequence | GenBank | KY417144.1 |
| Bat SARS coronavirus HKU3-7 genomic sequence | GenBank | GQ153542.1 |
| Bat coronavirus (BtCoV/279/2005) genomic sequence | GenBank | DQ648857.1 |
| Bat SARS-like coronavirus RsSHC014 genomic sequence | GenBank | KC881005.1 |
| Pangolin coronavirus isolate MP789 genomic sequence | GenBank | MT084071.1 |
| Pangolin coronavirus isolate PCoV_GX-P1E genomic sequence | GenBank | MT040334.1 |
| Pangolin coronavirus isolate PCoV_GX-P4L genomic sequence | GenBank | MT040333.1 |
| Bat SARS-like coronavirus isolate bat-SL-CoVZXC21 genomic sequence | GenBank | MG772934.1 |
| Bat SARS-like coronavirus isolate bat-SL-CoVZC45 genomic sequence | GenBank | MG772933.1 |
| Bat coronavirus RaTG13 genomic sequence | GenBank | MN996532.2 |
| SARS-CoV-2/human/SWE/01/2020 genomic sequence | GenBank | MT093571.1 |
| scRNA-seq dataset of immune cells from BALF of a healthy control | Morse et al., 2019 | GSE128033 |
| scRNA-seq dataset of immune cells from BALF of patients with COVID-19 and healthy controls | Liao et al., 2020 | GSE145926 |
| Experimental models: Cell lines | ||
| K562/HLA-E | Ulbrecht et al., 2000 | N/A |
| A549-hACE2 | O. Fernandez-Capetillo, Karolinska Insitute | N/A |
| Software and algorithms | ||
| NetMHC 4.0 | Andreatta and Nielsen, 2016; Nielsen et al., 2003 | https://services.healthtech.dtu.dk/service.php?NetMHC-4.0 |
| IEDB | Peters and Sette, 2005; Sidney et al., 2008 | http://tools.iedb.org/processing/ |
| FlowJo X | BD Biosciences | SCR_008520; https://www.flowjo.com/ |
| Prime | Jacobson et al., 2004 | SCR_014887; https://www.schrodinger.com/products/prime |
| Amber18 | Case et al., 2005 | SCR_014230; https://ambermd.org/ |
| Clustal Omega | EMBL-EBI | SCR_001591; https://www.ebi.ac.uk/Tools/msa/clustalo/ |
| iTOL | EMBL | SCR_018174; https://itol.embl.de/ |
| SCANPY | Wolf et al., 2018 | SCR_018139; https://scanpy.readthedocs.io/ |
| GSEAPY | Subramanian et al., 2005 | https://gseapy.readthedocs.io/ |
| R | The R Foundation | SCR_001905; https://www.rproject.org/ |
| GraphPad Prism | GraphPad Software, LLC. | SCR_002798; https://www.graphpad.com/ |
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