Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Goat anti-Human IgG Fc Cross-Adsorbed Secondary Antibody | Invitrogen | Cat# PI31413 |
| anti-IgD (Clone IA6-2) PE | BD Biosciences | Cat# 555779 |
| anti-IgM (MHM-88) PerCP-Cy5.5 | BioLegend | Cat# 314512 |
| anti-CD20 (Clone 2H7) APC-H7 | BD Biosciences | Cat# 560734 |
| anti-CD27 (Clone O323) PE-Cy7 | BioLegend | Cat# 302838 |
| anti-CD14 (Clone M5E2) PE/Dazzle™ 594 | BioLegend | Cat# 301852 |
| anti-CD16 (Clone 3G8) BV605 | BioLegend | Cat# 302040 |
| anti-IgG (Clone G18-145) BV650 | BD Biosciences | Cat# 740596 |
| anti-CD3 (Clone UCHT1) BUV737 | BD Biosciences | Cat# 612750 |
| anti-IL-2 (clone MQ1-17H12) FITC | Biolegend | Cat# 500304 |
| anti-CXCR5 (clone MU5UBEE) PerCP-eF710 | Invitrogen | Cat# 46-9185-42 |
| anti-IL-4 (clone MP4-25D2) PE | BioLegend | Cat# 500810 |
| anti-CD45RA (clone 5H9) PE-CF594 | BD Biosciences | Cat# 565419 |
| anti-TNF- a (clone Mab11) PE-Cy7 | E-Bioscience | Cat# 25-7349-82 |
| anti-CD40L (clone 24-31) BV421 | Biolegend | Cat# 310824 |
| anti-TCR-gd (clone B1.1) BV506 | Biolegend | Cat# 331220 |
| anti-CD4 (clone OKT4) BV605 | Biolegend | Cat# 317438 |
| anti-CD3 (clone SP34-2) BV650 | BD Biosciences | Cat# 563916 |
| anti-CCR7 (clone G043H7) BV711 | Biolegend | Cat# 353228 |
| anti-CD127 (clone A019D5) BV785 | Biolegend | Cat# 351330 |
| anti-IL-21 (clone 3A3-N2) APC | BioLegend | Cat# 513008 |
| anti-IFN-g (clone 4S.B3) A700 | Biolegend | Cat# 502520 |
| anti-CD25 (clone BC96) APC-Cy7 | Biolegend | Cat# 302614 |
| anti-CXCR3 (clone 1C6/CXCR3) BUV395 | BD Biosciences | Cat# 565223 |
| anti-CD8 (clone RPA-T8) BUV563 | BD Biosciences | Cat# 612914 |
| anti-CCR6 (clone 11A9) BUV737 | BD Biosciences | Cat# 612780 |
| anti-CD69 (clone FN50) BUV805 | BD Biosciences | Cat# 748763 |
| Purified anti-human CD66b (G10F5) | BioLegend | Cat#305102; RRID: AB_314494 |
| Purified anti-human CD57 (HNK-1) | BioLegend | Cat#359602; RRID: AB_2562403 |
| Purified anti-human HLA-DR (L243) | BioLegend | Cat#307651; RRID: AB_2562826 |
| Anti-Human CD19 (HIB19) - 142Nd | Fluidigm | Cat#3142001B |
| Anti-Human CD127 (A019D5) - 143Nd | Fluidigm | Cat#3143012B |
| Anti-Human IL4 (MP4-25D2) - 144Nd | Fluidigm | Cat#3144010B |
| Anti-Human CD4(RPA-T4) - 145Nd | Fluidigm | Cat#3145001B |
| Anti-Human IgD (IA6-2) - 146Nd | Fluidigm | Cat#3146005B |
| Anti-Human CD20 (2H7) - 147Sm | Fluidigm | Cat#3147001B |
| Anti-Human CD34 (581) - 148Nd | Fluidigm | Cat#3148001B |
| Anti-pSTAT6 (18/P-Stat6) - 149Sm | Fluidigm | Cat#3149004A |
| Anti-pSTAT5 (47) - 150Nd | Fluidigm | Cat#3150005A |
| Anti-Human CD123 (6H6) - 151Eu | Fluidigm | Cat#3151001B |
| Purified anti-human CD370 (CLEC9A/DNGR1) (8F9) - 152Sm | BioLegend | Cat#353802; RRID: AB_10983070 |
| Anti-pSTAT1 (4a) - 153Eu | Fluidigm | Cat#3153005A |
| Histone H3K27ac antibody (mAb) (MABI 0309) | ActiveMotiv | Cat#39685; RRID: AB_2793305 |
| Anti-Human CD27 (L128) - 155Gd | Fluidigm | Cat#3155001B |
| Anti-Human CD45 (HI30) - 156Gd | Fluidigm | Cat#3156010B |
| Purified anti-human CD25 (M-A251) | BioLegend | Cat#356102; RRID: AB_2561752 |
| Anti-Human pSTAT3 (4/P-Stat3) - 158Gd | Fluidigm | Cat#3158005A |
| Anti-Human CD11c (Bu15) - 159Tb | Fluidigm | Cat#3159001B |
| Anti-Human CD14 (M5E2) - 160Gd | Fluidigm | Cat#3160001B |
| Anti-Ki-67 (B56) - 161Dy | Fluidigm | Cat#3161007B |
| Purified anti-human CD1c (L161) | BioLegend | Cat#331502; RRID: AB_1088995 |
| Purified anti-human TCRg/d (B1) | BioLegend | Cat#331202; RRID: AB_1089222 |
| Anti-Human Arginase-1 (658922) - 164Dy | Fluidigm | Cat#3164012B |
| Anti-pCREB (87G3) - 165Ho | Fluidigm | Cat#3165009A |
| Purified anti-human CD16 (B73.1) | BioLegend | Cat#360702; RRID: AB_2562693 |
| Anti-Human CD38 (HIT2) - 167Er | Fluidigm | Cat#3167001B |
| Anti-Human CD8 (SK1) - 168Er | Fluidigm | Cat#3168002B |
| Anti-Human CD45RA (HI100) - 169Tm | Fluidigm | Cat#3169008B |
| Anti-Human CD3 (UCHT1) - 170Er | Fluidigm | Cat#3170001B |
| Anti-Human/ Mouse Granzyme B (GB11) - 171Yb | Fluidigm | Cat#3171002B |
| Anti-Human CD15 (W6D3) - 172Yb | Fluidigm | Cat#3172021B |
| Anti-Perforin antibody (B-D48) | abcam | Cat#ab47225 |
| Purified anti-human IFNg (4S.B3) | BioLegend | Cat#502502; RRID: AB_315227 |
| Anti-Cross Phospho-S6 (N7-548) - 175Lu | Fluidigm | Cat#3175009A |
| Anti-Human CD56 (NCAM16.2) - 176Yb | Fluidigm | Cat#3176008B |
| Anti-Human CD274/PD-L1 (MIH1) - 209Bi | Fluidigm | Cat#3209014B |
| Bacterial and virus strains | ||
| rVSV-ΔG-GFP/nanoluciferase | PMID: 35025672 | N/A |
| Pseudovirus expressing SARS-CoV-2 variants | In-house | Han et al.13, Suthar et al.14, Cohen et al.15 |
| Biological samples | ||
| Chemicals, peptides, and recombinant proteins | ||
| rhIFN-α | Miltenyi | Cat# 130-093-874 |
| Recombinant SARS-CoV-2 Wuhan spike protein | SinoBiological™ | Cat# 40589-V27B-B |
| Recombinant SARS-CoV-2 Omicron spike protein | SinoBiological™ | Cat# 40589-V49H3-B |
| DMSO | Sigma | D2650-100ML |
| Peptide cocktail for T-cell stimulation | In-house | Tarke et al.79 |
| Critical commercial assays | ||
| V-plex COVID-19 panel 23 | Mesoscale Discovery | Cat# K15567U |
| S-PLEX Human IFN-α2a kit | Mesoscale Discovery | Cat # K151P3S |
| Cell-ID 20-Plex Pd Barcoding Kit | Fluidigm | Cat#201060 |
| EQ™Four Element Calibration Beads | Fluidigm | Cat#201078 |
| Cell-ID™ Intercalator Ir | Fluidigm | Cat#201192A |
| One-Glo luciferase assay system | Promega | Cat# E6130 |
| Chromium NextGEM Chip J single Cell | 10x Genomics | 1000230 |
| Chromium NextGEM Single Cell Multiome ATAC + Gene Expression reagent bundle | 10x Genomics | 1000283 |
| Dual Index Kit TT Set A | 10x Genomics | 1000215 |
| Single Index Kit N Set A | 10x Genomics | 1000212 |
| Chromium X controller | 10x Genomics | 1000331 |
| NovaSeq 6000 S4 Reagent Kit V1.5 (200 cycles) | Illumina | 20028313 |
| Target 96 Inflammation Panel | Olink | |
| Bio-Rad protein assay kit II | Bio-Rad | 5000002 |
| Deposited data | ||
| scMultiome dataset - raw and processed data | This paper | GEO: GSE239799 |
| Blood transcriptomics dataset - raw and processed data | This paper | GEO: GSE239787 |
| Experimental models: Cell lines | ||
| Lenti-X 293T cells | Takara Bio | Cat. No. 632180 |
| 293T-ACE2-TMPRSS2 cells | In-house | Neerukonda et al.70 |
| Experimental models: Organisms/strains | ||
| Oligonucleotides | ||
| BCR primers | Liao HX et al. 75 | N/A |
| QIAseq SARS-CoV-2 Primer Panel | Qiagen Inc. | 333895 |
| QIAseq FX DNA Library Unique Dual Index Adapter Kit-A | Qiagen Inc. | 180479 |
| Recombinant DNA | ||
| pCAGGS Wuhan (SΔ19) | J. Craig Venter Institute – a gift from Dr. Gene S. Tan | N/A |
| pCAGGS Delta (B.1.617) | Sievers et al.69 | N/A |
| pCAGGS Omicron (B.1.529) | Sievers et al.69 | N/A |
| Software and algorithms | ||
| R 4.2.2; 4.1.1 | R Core Team102 | https://www.r-project.org/ |
| DESeq2 v1.38.3 | Love et al.101 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Seurat (R package) v4.0.5 | Hao et al.,86 Hafemeister et al.87 | https://satijalab.org/seurat/ |
| harmony (R package) v0.1.1 | Korsunsky et al.88 | https://portals.broadinstitute.org/harmony/index.html |
| ggraph (R package) v2.1.0 | Pedersen et al.98 | https://ggraph.data-imaginist.com/index.html |
| igraph (R package) v1.3.1 | Csardi et al.97 | https://igraph.org/ |
| Complexheatmap (R package) v2.12.0; 2.8.0 | Gu104 | https://jokergoo.github.io/ComplexHeatmap-reference/book/ |
| ArchR (R package) v1.0.1 | Granja et al.43 | https://www.archrproject.com/ |
| chromVAR (R package) v1.20.2 | Schep et al.96 | https://bioconductor.org/packages/release/bioc/html/chromVAR.html |
| fgsea (R package) v1.24.0 | Korotkevich et al.89 | https://bioconductor.org/packages/release/bioc/html/fgsea.html |
| limma (R package) v3.54.2 | Ritchie et al.93 | https://bioconductor.org/packages/release/bioc/html/limma.html |
| pcaMethods (R package) v1.84.0 | Stacklies et al.81 | https://bioconductor.org/packages/release/bioc/html/pcaMethods.html |
| FlowSOM (R package) v2.0.0 | Van Gassen et al.83 | https://bioconductor.org/packages/release/bioc/html/FlowSOM.html |
| Other | ||