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4 protocols using anti cd4 sk3

1

PBMC Cell Sorting and Characterization

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Cell sorting was performed from PBMC fractions using FACSAria II (Becton Dickinson) or Sony SH800 (Sony Biotechnology Inc.). For sorting, PBMC cells were stained with anti-CD3 (SK7, BD, cat. no 345767 or 557851), anti-CD4 (SK3, BD, cat. no 345770), anti-CD8 (SK-1, BD, cat. no 335822 or 345772) and the appropriate anti-Vβ antibody. Purities of the sorted cell fractions were controlled with flow cytometry, and the purities were nearly 100%.
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Multiparametric T Cell Immunophenotyping

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Mouse T cells were labeled for 20min at 4°C with anti-CD3 (17A2), anti-CD4 (GK1.5), anti-CD8 (53–6.7), anti-CD45.1 (A20), anti-CD45.2 (104), anti-Vβ5.1–5.2 (MR9–4), anti-CD44 (IM7), anti-CD62L (MEL-14), anti-CD127 (A7R34), KLRG1 (MAFA), anti-IFN-γ (XMG1.2) and anti-TNF-α (MP6-XT22) (all eBioscience). Human T cells were labeled with anti-CD3 (UCHT1, Beckman Coulter), anti-CD4 (SK3, BD Biosciences), anti-CD8 (SK1, BD Biosciences). Dead cells were excluded with 1ng/ml TO-PRO-3 iodide (Sigma-Aldrich), or Near-IR (L10119, Life Technology). Intracellular cytokine staining was performed with the cytofix/cytoperm kit (BD Biosciences). Flow cytometry analysis was performed on LSR-II and LSR Fortessa (BD Biosciences). Data were analyzed with FlowJo software (Tree Star, version 7.6.5 and version 10). Representative flow cytometry gating strategies are found in Fig S9.
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In Vitro SARS-CoV-2 T Cell Assay

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PBMCs were stimulated with peptide pools and expanded in vitro for 10 days as described before (23 (link)). Expanded T cell lines were stimulated for 5 hours at 37°C with or without SARS-CoV-2 peptide pools (2 μg/mL). After 1 hour, 10 μg/mL brefeldin A (MilliporeSigma) and 1× monensin (BioLegend) were added. Cells were stained with the yellow LIVE/DEAD fixable dead cell staining kit (Invitrogen, Thermo Fisher Scientific) and the surface markers anti-CD3 (SK7 or OKT3; BioLegend), anti-CD4 (SK3, BD Biosciences), and anti-CD8 (SK1, BD Biosciences). Cells were subsequently fixed and permeabilized using the Cytofix/Cytoperm kit (BD Biosciences) and stained with anti–IFN-γ (25723; R&D Systems) and anti–TNF-α (MAb11, BD Biosciences) antibodies and analyzed on a CytoFLEX (Beckman Coulter). Data were analyzed by FlowJo (BD Biosciences).
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Comprehensive Immune Cell Profiling from BAL Samples

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BAL samples were passed through a cell strainer to remove debris and any clumps of tissue. After washing, cell pellets were resuspended in 1 mL of RPMI-1640 (Thermo Fisher Scientific) and manually counted using a hemocytometer. Each sample was resuspended in FACS buffer (PBS plus 2% fetal bovine serum (Thermo Fisher Scientific) plus 10% human serum for 20 minutes on ice, followed by staining with LIVE/DEAD™ Fixable Near-IR Dead Cell Stain (Thermo Fisher) for 15 minutes in the dark to allow the exclusion of dead cells from the analysis. After washing, a cocktail of the antibodies listed below was added and staining completed in the dark for 25 minutes before fixing cells in 2% paraformaldehyde in PBS overnight. Samples were resuspended in FACS buffer, then analyzed on a BD LSRFortessa™ X-20 using BD FACS-Diva (BD Biosciences). Antibody cocktail (all antibodies from BD Biosciences): anti-CD3 UCHT1 BUV737, anti-CD4 SK3 (aka: Leu3a) BV480, anti-CD8 RPA-T8 PE, anti-CD19 HIB19 PerCP-Cy5.5, anti-CD45 HI30 BUV395, anti-CD56 NCAM16.2 BV711, anti-TCRγ/δ-1 11F2 FITC, MR1-5-OP-RU Tetramer (hereafter MR1-tetramer) conjugated to BV421-streptavidin (BD Horizon) was produced as described [6] .
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