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8 protocols using nk1 1 percp cy5

1

Multiparameter Flow Cytometry Analysis

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Cell suspensions were treated with anti CD16/CD32 (2.4G2) and then surface stained with combinations of the following fluorochrome-conjugated antibodies: From Biolegend: CD3e–FITC (clone: 145 2C11), Ly6C–FITC or APC/Cy7 (clone: HK1.4), Ly6G–PE/Cy7 (clone: 1A8), CD3e–APC/Cy7 (clone: 145 2C11), CD45R/B220–Pacific Blue (clone: RA3 6B2), CCR2-AlexaFluor647 (clone: SA203G11), CX3CR1-APC (clone: SA011F11), IgG2A,κ-APC isotype control; from BD Biosciences: NK1.1–PerCP/Cy5.5 (clone: PK136); from Ebiosciences: F4/80–APC (clone: BM8), CD4 (L3T4)–FITC (clone: RM4 5), CD11b–FITC (clone: M1/70), CD11b–PE (clone: M1/70), CD4–APC (clone: GK1.5). Cells were acquired on FACSCanto or AriaIII flow cytometers using FACSDiVa software, and data were analyzed using FlowJo software (Tree Star).
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2

Characterizing Gut Immune Responses in Mice

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Strains (5 × 108 CFU/day/mice) were administered by intragastric gavage to WT conventional BALB/c mice for 5 days. Colon samples were removed at sacrifice and stored in RNAlater® storage solution (Ambion, Life Technologies, Foster City, CA, USA) at − 80 °C until qRT-PCR analysis. MLN and intestine were harvested and immediately processed for flow cytometry. Cell suspensions of MLN and intestine (3–5 × 106 cells, in RPMI1640 supplemented by 10% FCS, 2 mM l-glutamine, 2 mM HEPES, 40 mg/ml gentamycine) were stimulated using the Leukocyte Activation Cocktail containing BD GolgiPlug (BD Biosciences) (1 μl/ml of cell suspension) for 5 h. Cells were stained by mAbs anti-mouse CD11c eFluor450, CD11b eFluor 450, B220 eFluor 450, CD3 eFluor 450, CD117 Alexa Fluor 700, NK1.1 PerCP-Cy5.5, NKp46 FITC (provided by eBioscience), CD4 APC-H7, CD90.2 BV 500; CD45RB BV 605, MHCII BV 650 (provided by BD Bioscience, san Jose, CA, USA). Subsequently, cells were permeabilized and fixed using the Transcription Factor Buffer Set (BD Bioscience), and intracellular staining was performed using mAbs anti-IL-17A eFluor450, anti-FOXP3 PE-Cy7, anti-IL-22 PE and RORgt APC (eBioscience). Flow cytometry data were analyzed using software FlowJo. Gating strategy and representative dot plots for control and BIO5768 treated mice are presented in Figs. S1 and S2.
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3

Activation of Splenocytes by IL-15 and BI-1347

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Splenocytes were cultured in RPMI1640 supplemented with 10% FBS, 10 mmol/l HEPES, 15 mmol/l sodium pyruvate, 1% penicillin/streptomycin and 0.57 μmol/l β-mercaptoethanol and treated with either 2.5 ng/ml IL-15, 150 nmol/l BI-1347 or the combination thereof and incubated for 44 h in an incubator as described above. Protein Transport Inhibitor Cocktail (eBioscience) was added for the last 4 h at 37°C. Separate aliquots of the cells were analyzed by Western blotting and flow cytometry using the following antibodies: CD3epsilon (eFluor 450), NK1.1 (PerCP-Cy5.5) and granzyme B (PE) (eBioscience). Intracellular staining was performed using fixation and permeabilization buffer (eBioscience). Stained cells were collected and analyzed with a FACS Canto II instrument.
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4

Liver Macrophage Phenotyping in Mice

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Liver tissues from male C57BL/6J mice were minced and digested for 30 min at 37 °C with type II collagenase (Sigma-Aldrich) in PBS containing 2% BSA (pH 7.4). The cell suspension was filtered and then spun at 3000 rpm for 5 min to separate the floating liver tissue fraction from the stromal vascular cell (SVC) pellet. The SVCs were resuspended in PBS supplemented with 2% FBS and incubated with Fc-Block (BD Bioscience).
To determine macrophage phenotype fluorescence-activated cell sorting analysis FACSAriaII (BD Bioscience) was performed using following antibodies, NK1.1-PerCP Cy5.5 (eBioscience, San Diego, CA), CD3-PerCP Cy5.5 (eBioscience, San Diego, CA), CD19-PerCP Cy5.5(eBioscience), TER119-PerCP Cy5.5 (eBioscience, San Diego, CA), CD45-APC-Cy7(eBioscience, San Diego, CA), Gr-1Fluor450 Ly-6G(PB) (eBioscience, San Diego, CA), F4/80-PE-Cy7(Bio Legend, San Diego, CA), CD11b-PETR (Invitrogen, Carlsbad, CA, USA), CD11c-PE(eBioscience, San Diego, CA), CD206 Alexa Fluor 647 (Bio Legend, San Diego, CA). Data analysis and compensation were performed using FlowJo (Tree Star).
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5

Isolation and Phenotyping of Murine Lymphocytes

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The mice were sacrificed by cervical dislocation. The liver and splenic lymphocytes were isolated as done previously with minor modifications (31 (link), 32 (link)). In brief, livers and spleens were homogenized and washed two times with the RPMI-1640 medium (300 × g for 10 min at 4°C). The OptiPrepTM working solution (OPWS)-40% iodixanol (Sigma Chemical, St. Louis, Mo., USA) was added to the liver pellets and then layered with Hank's balanced salt solution (Sigma) while the red blood cell lysing buffer (Sigma R7757) was added to the spleen pellets. The pellets were then washed at least two times with the RMPI-1640 medium (300 × g for 7 min at 4°C) and stained with anti-mouse antibodies, including CD3-Alexa 700, CD4-APC/Cy7 or CD4-FITC, CD8-PE/Cy7, NK1.1-PerCP/Cy5.5, CD25-PE, IFNγ-Alexa Fluor 488, IL4-PE, IL17-Alexa Fluor 647, and FOXP3-APC (all from eBioscience). The staining procedures and analyses were performed according to the manufacturer's protocol. The samples were analyzed by the FACSCalibur flow cytometer (BD Biosciences) as previously described (39 (link)).
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6

Comprehensive Murine Immune Cell Profiling

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Mouse cells were preincubated with purified antimouse CD16/CD32, and human cells were incubated with FcR-blocking reagent (BD Biosciences). Isolated cells were stained with labeled antibodies in phosphate-buffered saline (PBS) with 1% bovine serum albumin (BSA). Dead cells were excluded based on staining with Live/Dead fixable dye (eBioscience). Forkhead box P3 (FOXP3) fixative solution (eBioscience) was used for FOXP3 staining. Prepared samples were analyzed using a flow cytometer (FACSCalibur or FACSAria; BD Biosciences). Data were analyzed using FlowJo software (TreeStar, Ashland, OR, USA). The following beads and antibodies were used: OneComp eBeads (eBioscience), antimouse CD11c Brilliant Violet 421 (BioLegend), antimouse CD11b PE-cy7 (eBioscience), GR1-APC (eBioscience), LY6C-APC-eFluor (eBioscience), F4/80 PE (eBioscience), NK-1.1 Percp-Cy5.5 (eBioscience), anti-CD45 FITC (eBioscience), Live/Dead Aqua (eBioscience), anti-CD4 eFluor 450 (eBioscience), anti-CD8 APC eFluor 780 (eBioscience), anti-CD3 Percp-Cy5.5 (eBioscience), anti-CD19 PE-CY7 (eBioscience), anti-CD25 APC (eBioscience), anti-Foxp3 PE (eBioscience), and anti-CD3 APC (BioLegend).
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7

Multiparameter Flow Cytometry Analysis

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Cell suspensions were treated with anti CD16/CD32 (2.4G2) and then surface stained with combinations of the following fluorochrome-conjugated antibodies: From Biolegend: CD3e–FITC (clone: 145 2C11), Ly6C–FITC or APC/Cy7 (clone: HK1.4), Ly6G–PE/Cy7 (clone: 1A8), CD3e–APC/Cy7 (clone: 145 2C11), CD45R/B220–Pacific Blue (clone: RA3 6B2), CCR2-AlexaFluor647 (clone: SA203G11), CX3CR1-APC (clone: SA011F11), IgG2A,κ-APC isotype control; from BD Biosciences: NK1.1–PerCP/Cy5.5 (clone: PK136); from Ebiosciences: F4/80–APC (clone: BM8), CD4 (L3T4)–FITC (clone: RM4 5), CD11b–FITC (clone: M1/70), CD11b–PE (clone: M1/70), CD4–APC (clone: GK1.5). Cells were acquired on FACSCanto or AriaIII flow cytometers using FACSDiVa software, and data were analyzed using FlowJo software (Tree Star).
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8

Multiparameter Flow Cytometry Staining

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Samples were stained with a 2.4G2 blocking antibody and monoclonal antibodies in 1% PBS-serum for 20 minutes on ice in the dark. For samples stained with CD1 tetramer, cells were incubated for 15 minutes at room temperature in the dark, followed by 15 minutes on ice in the dark. Samples requiring intracellular staining were then fixed and permeabilized using CytoFix/CytoPerm (BD Biosciences) and stained with intracellular antibodies for 15 minutes on ice in the dark. Events were collected on either a FACSAria (BD Biosciences) or a MACSQuant (Miltenyi Biotec). Data were analyzed using FlowJo (Tree Star Inc.). IL-17A-AlexaFluor488, CD45.2-FITC, HSA-FITC, TCRβ-FITC, TCRVβ2-FITC, CD45.1-PE, PLZF-PE, TCRβ-PE, Foxp3-PE-Cy5.5, NK1.1-PerCPCy5.5, TCRβ-PErCPCy5.5, RORγt-PerCPeFluor710, TCRβ8.1/2-PerCPeFluor710, Ly49G2-PerCPeFluor710, IFN-γ-PE-Cy7, NK1.1-PE-Cy7, T-Bet-PE-Cy7, CD45.1-APC, CD25-APC, IL-4-APC, CD4-APCeFluor780, CD44-APCeFluor780, CD45.2-APCeFluor780, CD90.1-APCeFluor780, CD8α-eFluor450, CD3-eFluor450, Ki67-eFluor450, and TNF-α-eFluor540 were purchased from eBioscience (San Diego, CA). Ly49C/I-FITC, Ly49A/D-PE, and CD4-PerCP were purchased from BD Pharmingen. TCRVβ7-PE was purchased from Biolegend. CD1d tetramer loaded with α-GalCer, CD1d tetramer loaded with PBS-57 as well as unloaded controls were provided by the NIH Tetramer Facility.
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