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5 protocols using cd69 clone fn50

1

Isolation and Phenotyping of Human ILCs

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Lung cells from HSPC-engrafted MISTRG mice were isolated as described above. Cell surface staining with fluorescent antibodies was performed as previously described [17 (link), 18 (link)]. The following antibodies were used for flow cytometry: CD127 (clone A019D5, Biolegend), CRTH2 (clone BM16, Biolegend), CD94 (clone DX22, Biolegend), CXCR4 (clone 12G5, Biolegend), CXCR6 (clone K041E5, Biolegend), GITR (clone 108-17, Biolegend), CD16 (clone 3G8, Biolegend), CD69 (clone FN50, Biolegend), CD117 (104D2D1, Beckman Coulter), HLA-DR (clone G46-6, BD Biosciences), CD2 (clone RPA-2.10, BD Biosciences), CD56 (clone NCAM16.2, BD Biosciences), CD81 (clone JS-81, BD Biosciences), CD94 (clone HP-3D9, BD Biosciences), CD98 (clone UM7F8, BD Biosciences), CD103 (clone Ber-ACT8, BD Biosciences), and CD45RA (clone HI100, BD Biosciences). In all experiments, ILCs were defined as human CD45+Lin-CD3TCRαβCD127+CD94 cells. Lineage markers included CD14 (clone M5E2, Biolegend), CD19 (clone HIB19, Biolegend), CD11c (clone Bu15, Biolegend), CD123 (clone 6H6, Biolegend), FcεRIα (clone AER-37 (CRA-1), Biolegend), CD34 (clone 581, BD Biosciences), TCRαβ (clone IP26) and CD3 (clone SK7).
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2

Flow Cytometry Analysis of T-cell Epitopes

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Unless otherwise specified, flow cytometry in this study was performed with a MACSQuant VYB cytometer (Miltenyi Biotec). T-cells were assessed for surface presentation of epitopes using fluorescently labeled monoclonal antibodies for CD69 (clone FN50, BioLegend), or DYKDDDDK (clone L5, BioLegend; or #130–101-571, Miltenyi Biotec). EGFRt expression was measured with Erbitux (Bristol-Myers Squibb) biotinylated in-house (EZ-link Sulfo-NHS-Biotin, Pierce) followed by PE-conjugated streptavidin (Jackson ImmunoResearch). Flow data were analyzed and gated in FlowJo (TreeStar) (see Supplementary Fig. 8 for an example of gating strategy). Unless otherwise noted, data shown are drawn from biological triplicates (i.e., three distinct samples).
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3

PBMC Immune Phenotyping Protocol

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PBMC were thawed and divided in two 96-well plates for immune phenotyping. Surface staining was performed with the following antibodies: CD3 (clone SP34-2), from BD Biosciences, CD4 (clone OKT-4) and β7 integrin (clone FIB504) from Invitrogen, CD8 (clone SK1) and PD-1 (clone EH12.2H7) from Biolegend and LAG3 (clone P18627), and TIM3 (Clone 344823) from R&D. Intracellular staining was performed using the Foxp3 / Transcription Factor Staining Buffer Set (Ref. LTI 00-5523-00, Invitrogen) according to manufacturer’s instructions and using the following antibodies: granzyme A (clone CB9), T-bet (clone eBio4B10) and Eomes (clone WD1928) from Invitrogen and Granzyme B (clone GB-11) from Sanquin and perforin (clone Pf-344) from MabTech). Cells from the stimulation assay were characterised through surface staining using the following antibodies: CD3 (clone SP34-2), from BD Biosciences, CD4 (clone OKT-4) from Invitrogen, CD8 (clone SK1) and CD69 (clone FN50) from Biolegend (Supplementary Table 3). Samples were acquired on LSRII flow cytometer (BD Biosciences) using the DIVA Software and data was analysed using FlowJo software. Gating strategies are shown in Supplementary Figures 6–8.
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4

Immune Cell Profiling Protocol

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After 18 h, supernatants were collected and cells detached using ice-cold PBS-EDTA, and stained using the following conjugated antibodies for surface markers: CD14 (clone M5E2, Biolegend), CD16 (clone NKP15, BD Biosciences), CD25 (clone M-A251, BD Biosciences), CD11b (clone ICRF44, Biolegend), CD80 (clone L307.4, BD Biosciences), CD69 (clone FN50, Biolegend). Dead cells were excluded with with Fixable Viability Dye BV421 (BD Biosciences). Samples were run on a BD Fortessa flow cytometer and data analysed using FlowJo software (BD Biosciences).
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5

Flow Cytometry Analysis of T-cell Epitopes

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Unless otherwise specified, flow cytometry in this study was performed with a MACSQuant VYB cytometer (Miltenyi Biotec). T-cells were assessed for surface presentation of epitopes using fluorescently labeled monoclonal antibodies for CD69 (clone FN50, BioLegend), or DYKDDDDK (clone L5, BioLegend; or #130–101-571, Miltenyi Biotec). EGFRt expression was measured with Erbitux (Bristol-Myers Squibb) biotinylated in-house (EZ-link Sulfo-NHS-Biotin, Pierce) followed by PE-conjugated streptavidin (Jackson ImmunoResearch). Flow data were analyzed and gated in FlowJo (TreeStar) (see Supplementary Fig. 8 for an example of gating strategy). Unless otherwise noted, data shown are drawn from biological triplicates (i.e., three distinct samples).
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