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3 protocols using anti pe and anti apc magnetic beads

1

SARS-CoV-2 Antigen-Specific T Cell Profiling

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Cryopreserved samples containing 1-10 × 107 PBMC from DRB1*07:01 (DR7)+ convalescent subjects or pre-pandemic negative controls were thawed, washed twice with PBS containing 2% FBS, and resuspended in either complete EHAA or RPMI 1640 with 5% FBS. Staining with a pre-mixed cocktail of DR7:p-streptavidin-PE, DR7:p-streptavidin-PE-Cy7, and DR7:p-streptavidin-APC tetramers at a final concentration of 10 nM for each reagent was for 1 hour at room temperature. Anti-PE and anti-APC magnetic beads (Miltenyi Biotec) were then added, and bead-bound cells were enriched as previously described (22). Cells in the bound and unbound fractions were stained with Zombie Aqua viability dye (BioLegend) and a surface marker antibody panel consisting of anti-CD20BV510 (clone 2H7, BioLegend), anti-CD14BV510 (clone M5E2, BioLegend), anti-CD3AF700 (clone UCHT1, BioLegend), anti-CD4BV605 (clone OKT4, BioLegend), anti-CD8BUV395 (clone RPA-T8, BioLegend), anti-CD45ROAPC/Cy7 (clone UCHL1, BioLegend), anti-CXCR3PE/Dazzle594 (clone G025H7, BioLegend), anti-CXCR5BV421 (clone J252D4, BioLegend), anti-PD-1BV785 (clone EH12.2H7, BioLegend), and anti-CCR4PerCP/Cy5.5 (clone L291H4, BioLegend) for 30 min at room temperature. Data were acquired on an LSR Fortessa X-20 (BD) flow cytometer and analyzed with FlowJo software (BD).
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Multiparametric Flow Cytometry Profiling of Antigen-specific CD8+ T Cells

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Samples from HLA-A2–positive subjects were dual stained with a mixture containing a pool of PE and APC tetramers, PBMCs (20 ×10^6) were stained simultaneously with 3 μl each in 200 μl of PBS supplemented with 2% BSA and incubated for 15 min at 37°C. Cells were then incubated with 30 μl each of anti-PE and anti-APC magnetic beads (Miltenyi Biotec, San Diego, CA, USA) and enriched on a MS-sized magnetic column according to the manufacturer’s instructions. After enrichment, flow-through cells were reserved for bulk memory and naive CD8+ T-cell sorting described in the following section. Both enriched and flowthrough cells samples were washed and then stained for 30 min at 4°C with 5 μl each:anti- CD8+ BV605(Biolegend), AF700 CD45RA(BD Bioscience), APC-Cy7 CCR7(Biolegend), PerCP- eFluor 710 TIGIT(eBioscience), PE-Cy7 PD-1(Biolegend), BV650 CD95(Biolegend), BV421 KLRG1(Biolegend), 2.5 μl each of anti-CD4/CD14/CD16/CD20/CD40-FITC (dump channel; eBioscience, Waltham, MA, USA), and 1:10,000 syTOX green viability dye(Thermo Fisher). CD8+ cells were sorted using a FACSAria II(BD Biosciences) into lysis buffer from an Allprep DNA RNA mini prep kit (Qiagen) and processed for DNA and RNA according to the manufacturer’s instructions.
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3

Multiparametric Flow Cytometry Profiling of Antigen-specific CD8+ T Cells

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Samples from HLA-A2–positive subjects were dual stained with a mixture containing a pool of PE and APC tetramers, PBMCs (20 ×10^6) were stained simultaneously with 3 μl each in 200 μl of PBS supplemented with 2% BSA and incubated for 15 min at 37°C. Cells were then incubated with 30 μl each of anti-PE and anti-APC magnetic beads (Miltenyi Biotec, San Diego, CA, USA) and enriched on a MS-sized magnetic column according to the manufacturer’s instructions. After enrichment, flow-through cells were reserved for bulk memory and naive CD8+ T-cell sorting described in the following section. Both enriched and flowthrough cells samples were washed and then stained for 30 min at 4°C with 5 μl each:anti- CD8+ BV605(Biolegend), AF700 CD45RA(BD Bioscience), APC-Cy7 CCR7(Biolegend), PerCP- eFluor 710 TIGIT(eBioscience), PE-Cy7 PD-1(Biolegend), BV650 CD95(Biolegend), BV421 KLRG1(Biolegend), 2.5 μl each of anti-CD4/CD14/CD16/CD20/CD40-FITC (dump channel; eBioscience, Waltham, MA, USA), and 1:10,000 syTOX green viability dye(Thermo Fisher). CD8+ cells were sorted using a FACSAria II(BD Biosciences) into lysis buffer from an Allprep DNA RNA mini prep kit (Qiagen) and processed for DNA and RNA according to the manufacturer’s instructions.
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