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14 protocols using anti nk1.1 pk136

1

NK Cell-Mediated Cytotoxicity Assay

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YAC-1 cells were labelled with 0.5 μM carboxyfluorescein succinimidyl ester (CFSE) (Invitrogen) for 20 min at room temperature. Subsequently, the labelled YAC-1 cells were incubated with enriched NK cells at effector-to-target ratios as indicated for a total time of 4 h 30 min. Anti-CD107a antibody (1D4B; BD Biosciences) was present from the beginning of the coculture. After the assay, the cells were stained with anti-NK1.1 (PK136; BioLegend), anti-CD3 (145-2C11), and LIVE/DEAD Fixable Aqua Dead Cell Stain Kit (Invitrogen). The percentages of live target cells were calculated based on the numbers of cells negative for the live/dead marker in each sample over total CFSE positive cells in the samples without NK cells. All experiments were run in triplicates.
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2

Quantitative Analysis of T Follicular Helper Cell Migration

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For enrichment of CD4+ T cells, total splenocyte samples from WT and Rictor−/− mice at day 8 after infection with LCMV were subjected to depletion of cells that were positive for lineage markers (Lin+ cells) using biotin-conjugated antibodies [anti-CD8 (53–6.7), anti-B220 (RA3-6B2), anti-CD11c (N418), anti-Gr-1 (RB6-8C5), anti-TER119 (TER-119), and anti-NK1.1 (PK136), all from Biolegend] coupled to the BeaverBeads Mag500 Streptavidin Matrix (22302, Beaver). The surfaces of the Lin cells were then stained with anti-CD4, anti-CD44, anti-GITR, anti-CD25, and anti-CXCR5 to identify TFH cells. Next, 4 × 105 TFH cells from WT or Rictor−/− mice were loaded into the upper chamber of a 24-well transwell plate (5-µm pore, Corning), and 600 µl of chemotaxis medium supplemented with or without the CXCL13 (4 µg/ml, 4583906, Biolegend) was added to the lower chamber. The cells were allowed to migrate for 3 h in a 5% CO2 incubator at 37°C. Then, all the migrated cells were collected from the lower chamber, and the numbers of migrated TFH cells were determined by flow cytometry (FACS Canto II). Based on the absolute number of TFH cells, the “net migration (% of input)” was calculated as follows: Net migration (% of input) = (# of migrated TFH cells to CXCL13 − # of migrated TFH cells in the absence of CXCL13)/(# of TFH cells in the input sample).
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3

Multiparametric Flow Cytometry Analysis

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The harvested spleens were mashed and single-cell suspensions of the spleens were stained with the following surface antibodies: anti-CD45 (30-F11, BD Biosciences), LIVE/DEAD Fixable Blue cell stain (Invitrogen), anti-CD19 (ID3, BD Biosciences), anti-CD8a (53-6.7, BioLegend), anti-CD27 (LG7F9, eBioscience), anti-CD11b (M1/70, BioLegend), anti-CD11c (HL3, BD Biosciences), anti-CD86 (GL1, BioLegend), anti-NK1.1 (PK136, BioLegend), anti-NKp46 (29A1.4, BioLegend), anti-MHC Class II (M5/114.15.2, BD Biosciences), anti-F4/80 (BM8, BioLegend), anti-CD80 (16-10A1), anti-CD3 (17A2, BioLegend), anti-CD4 (RM4-5, Invitrogen), anti-CTLA-4 (UC10-4B9, BioLegend), anti-PD-1 (29F.1A12, eBioscience), anti-CD28 (37.51, BioLegend), anti-CD44 (IM7, BD Biosciences), anti-CD43 (1B11, BioLegend), anti-CD47 (miap301, BioLegend), anti-CD62L (MEL-14, BioLegend), anti-CD25 (PC61.5, eBioscience), and anti-CD107a (1D4B, BioLegend). Intracellular staining was then performed with a FOXP3 permeabilization and fixation kit (eBioscience) according to manufacturer’s recommendations using the following antibodies: Ki-67 (B56; BD Biosciences) and GrB (QA16A02, BioLegend). Flow cytometric data were collected with a Beckman Coulter Cytoflex LX (6-L NUV) flow cytometer and analyzed using FlowJo software (Tree Star).
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4

NK Cell Stimulation and Functional Assays

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CD49b+ NK cells were enriched by magnetic sorting (Miltenyi) from BM. For stimulation through NK1.1, 10 µg/ml anti-NK1.1 (PK136, 108701; BioLegend) in NaHCO3 (pH 9.2) was precoated on an ELISA plate (655081; Greiner Bio-One). After culture in 20 ng/ml murine IL-15 (210-15; PeproTech) overnight, NK cells were then added to the plate with Brefeldin A (555029; BD Biosciences) for the last 4.5 h. For stimulation through cytokines, NK cells were cultured with 1,000 U/ml IL-2 (212-12; PeproTech) and 10 ng/ml IL-12 (210-12, PeproTech) overnight and Brefeldin A for the last 4.5 h. Cytofix/Cytoperm Fixation/Permeabilization Kit (554714; BD Biosciences) was used to detect IFN-γ (XMG1.2, 12-7311-81; eBioscience), and Cyto-Fast Fix/Perm Buffer Set (426803; BioLegend) was used to detect GZMB (QA16A02, 372207; BioLegend) according to the manufacturer’s instructions.
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5

Comprehensive Immune Cell Profiling Protocol

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The following primary antibodies and factors were used in this study: anti‐vitronectin (ab45139, Abcam, Cambridge, MA; MAB38751, R&D Systems, Inc., Minneapolis, MN), anti‐thrombospondin 1 (Ab‐11, Thermo Scientific, Hudson, NH; ab1823, ab3131, Abcam), anti‐FX (H‐120 and C‐20, Santa Cruz Biotechnology, Santa Cruz, CA), anti‐fibrinogen (CSI19761A, Cell Sciences Inc., Canton, MA), anti‐albumin (A90‐134A, Bethyl Laboratories, Inc., Montgomery, TX), anti‐CD45 (ab10558, Abcam; M0701, DAKO, Carpinteria, CA), anti‐CD11b (BD Biosciences, San Jose, CA), anti‐MECA32 Ab (BD Biosciences), anti‐αSMA (M0851, DAKO), anti‐CD4 (RM4‐5, BD Biosciences), anti‐CD8a (53–6.7, BioLegend, San Diego, CA), anti‐CD11c (HMα2, BioLegend), anti‐B220 (RA3‐6B2, BioLegend), anti‐NK‐1.1 (PK136, BioLegend), anti‐TCRβ (H57‐597, BD Biosciences) and anti‐IFNγ antibodies (Santa Cruz Biotechnology). CCL2, VEGF, TNFα, G‐CSF and SDF1 were purchased from R&D Systems (Minneapolis, MN). IL‐6 and CXCL1 (Miltenyi Biotec, Bergisch Gladbach, Germany), TGF‐β (Peprotech) and HGF Wako Pure Chemical Industries) were used.
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6

Isolation and Characterization of TFH Cells

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TFH cells were isolated using a previously described method.15 (link) Briefly, total splenocytes obtained from WT and Ezh2fl/flCd4-Cre mice on day 8 after LCMV Armstrong infection were subjected to the depletion of lineage marker-positive cells (Lin+ cells) using biotin-conjugated antibodies (anti-B220 (RA3–6B2), anti-CD8 (53.6.7), anti-CD11c (N418), anti-TER-119 (TER-119) and anti-NK1.1 (PK136); all from BioLegend), followed by coupling to BeaverBeads Mag500 Streptavidin (22302; Beaver). The enriched Lin cells were then stained with anti-CD4, anti-CD44, anti-GITR, anti-CD25 and anti-CXCR5 antibodies (all identified in Supplementary Table 3). The CD4+CD25GITRCD44+CXCR5+ TFH cells were sorted with a FACS Aria II cell sorter (BD Biosciences) and then immediately lysed with TRIzol LS reagent (10296; Life Technologies). Then, total RNA was extracted and submitted to CapitalBio for a microarray analysis.
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7

Immune Cell Stimulation and Analysis

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Functional grade anti-CD3 (145-2C11), anti-CD28 (37.51), anti-IL-4 (11B11), and anti-IFN-γ (H22) were purchased from BioXCell (West Lebanon, NH, USA). Fluorescently labeled anti-B220 (RA3-6B2), anti-CD3 (17A2), anti-CD4 (RM4-5), anti-CD8 (53-6.7), anti-CD11b (M1/70), anti-CD11c (N418), anti-CD25 (PC61), anti-NK1.1 (PK136), and anti-TCR-β (H57-597) were purchased from BioLegend (San Diego, CA, USA). Fluorescently labeled anti-phospho-c-Jun (Ser63) (KM-1) was obtained from Santa Cruz Biotechnology (Santa Cruz, CA, USA), and anti-ATF4 (D4B8), anti-GRP78, anti-PERK (C33E10), anti-phospho-PERK (16F8), anti-eIF2a (D7D3), anti-phospho-eIF2a (Ser51) (D9G8), anti-phospho-p65 (Ser536) (93H1), anti-IκBα, anti-phospho-IκBα (Ser32), and anti-phospho-Erk1/2 (Thr202/Tyr204) (D13.14.4E) were provided by Cell Signaling Technologies (Danvers, MA, USA). FAT10, UBA6, and USE1 antibody were described previously [9 (link),10 (link),13 (link)]. The recombinant murine IL-1β (rmIL-1β), IL4, IL-6, IL-12p70, IL-23, and TGF-β1 were purchased from BioLegend (San Diego, CA, USA).
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8

Multiparameter Flow Cytometry of Immune Cells

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Isolated cells from thymic glands, PDLNs, and spleens were stained with the following antibodies: anti‐CD11b (M1/70; BioLegend), anti‐CD11c (N418; BioLegend), anti‐PDCA‐1 (129c1; BioLegend), anti‐Ly6G (1A8; BioLegend), anti‐CD8ɑ (53‐6.7; BD BioSciences), anti‐B220 (RA3‐6B2; BioLegend), anti‐CD19 (1D3; BD BioSciences), anti‐CD19 (6D5; BioLegend), anti‐CD5 (53‐7.3; BD BioSciences), anti‐CD21 (7E9; BioLegend), anti‐CD3 (17A2; BioLegend), anti‐NK1.1 (PK136; BioLegend), anti‐NKp46 (29A1.4; BioLegend), and anti‐IFN‐γ (XMG1.2; BioLegend). Dilutions, catalogue numbers, and RRIDs of antibodies are given in Table S1. The stained cells were analyzed by a LSR Fortessa at the BioVis core facility, Uppsala University, Uppsala, Sweden. Single stained, unstained, and Fluorescence Minus One controls were applied as negative controls to identify any spread of the fluorochromes into the channel of interest and to properly gate the fluorochromes. The data were analyzed by Flowlogic software (Inivai Technologies). Gating strategies for flow cytometric analysis for different cell types are shown in Figures S2‐S6.
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9

Comprehensive Immune Cell Profiling

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For cell sorting and flow cytometry analysis, cell suspension were prepared as described above, incubated with fixable viability dye and subsequently stained with following fluorophore-conjugated monoclonal antibodies: anti-CD45 (30-F11, BD Biosciences), anti-CD45.2 (104, Biolegend), anti-CD90.2 (thy1.2) (53–2.1, Biolegend), anti-CD3 (17A2, Biolegend), anti-CD4 (Biolegend, RM4–5), anti-CD8 (53–6.7, Biolegend), anti-CD11b (M1/70; Biolegend), anti-CD11c (N418, Biolegend), anti-Ly6C (HK1.4, Biolegend), anti-Ly6G (1A8, BD Biosciences), anti-Siglec-F (E50–2440, BD Bioscience), anti-mouse MHC Class II (I-A/I-E) (M5/114.15.2, eBioscience), anti-NK1.1 (PK136, Biolegend), anti-CD19 (6D5, Biolegend), anti-T1/ST2 (DJ8, MD Biosciences), anti-KLRG1 (2F1, Biolegend), anti-FoxP3 (FJK-16S, eBiosciences), anti-Ki-67 (16A8, Biolegend), anti-Gata3 (TWAJ, eBioscience), anti-IL13 (eBio13A, eBioscience), anti-IFNgR1 (XMG1.2, BD Bioscience).
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10

Multiparametric Flow Cytometry Profiling

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For cell surface staining, cells were pre-incubated with 2.4G2 Fcγ RII/RIII blocking mAb for 15 minutes and then stained with the appropriate combinations of mAbs diluted in HBSS + 2% FBS for 30 minutes at 4°C. Cells were analyzed on a BD FACS CantoII, or Cytek Aurora Spectral Cytometer and data were processed with FlowJo software (TreeStar). The complete list of antibodies use is as follows: anti-human Vβ5.1 (LC4, Invitrogen), anti-TCRβ (H57–597, BioLegend), anti-CD44 (IM7, BioLegend), anti-Vβ11 (KT11, BioLegend), anti-CD45.2 (104, BioLegend), anti-CD45.1 (A20, BioLegend), anti-SiglecF (E50–2440, BD Bioscience), anti-CD45 (30-F11, BioLegend), anti-CD11c (N418, BioLegend), anti-CD11b (M1/70, BioLegend), anti-Ly6G (1A8, BioLegend), anti-CD19 (6D5, BioLegend), anti-NK1.1 (PK136, BioLegend), anti-CD3 (17A2, BioLegend), Zombie Red (BioLegend), anti-mouse CD185/CXCR5 (L138D7, Biolegend), anti-mouse CD279/PD-1 (29F.1A12, Biolegend), and anti-Ki67 (SolA15, Invitrogen).
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