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12 protocols using anti cd8a 53 6

1

Immunofluorescence Staining of Liver Tissue

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For immunofluorescence staining, 5μm frozen liver tissue sections were fixed with 3% PFA and blocked with species-specific serum (Sigma-Aldrich, Steinheim, Germany). Sections were incubated with specific antibodies for 1h at RT. The following antibodies were used: anti-cCaspase3 (Cell Signaling Technologies, Danvers USA), anti-CD3e (145-2C11, Becton Dickinson (BD) Biosciences, Heidelberg, Germany), anti-CD4 (RM4-5, Biolegend, San Diego, USA), anti-CD8a (53–6.7, Biolegend, San Diego, USA), anti-CD68 (AbD Serotec, Düsseldorf, Germany), anti-Ly6G and Ly6C (RB6-8C5, BD Biosciences, Heidelberg, Germany), and anti-Ki67 (MMI, Leica Biosystems, Wetzlar, Germany). Slides were washed and incubated with fluorochrome conjugated second stage antibody and DAPI (Sigma Aldrich, Steinheim, Germany) for 30min. The following second stage antibodies were used: anti-armenian-hamster-IgG-AlexaFluor®488, anti-armenian-hamster-IgG-Cy3, anti-rabbit-IgG-DyLight®549, anti-rat-IgG-DyLight®549 (all Dianova, Hamburg, Germany), and anti-rat-IgG-Alexa Fluor®488 (Life Technologies, Darmstadt, Germany). Stained sections were mounted with ProLong Gold Antifade Reagent (Invitrogen) and analyzed using an Observer.Z1 attached to an AxioCam MRm camera, an Plan-Apochromat 40x/1,3 NA and 100x/1,4 NA oil objective and the AxioVision Software (all Zeiss Microscopy).
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2

Multimodal Analysis of Immune Cells

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Cells were isolated 72 hours after injection with LNPs unless otherwise noted. Mice were perfused with 20 mL of 1X PBS through the right atrium. Liver and lung tissues were finely minced, and then placed in a digestive enzyme solution with Collagenase Type I (Sigma Aldrich), Collagenase XI (Sigma Aldrich) and Hyaluronidase (Sigma Aldrich) at 37 ºC at 550 rpm for 45 minutes4,5. The spleen, bone marrow and thymus tissues were placed in 1X PBS solution. Cell suspension was filtered through 70μm mesh and red blood cells were lysed. Cells were stained to identify specific cell populations and sorted using the BD FacsFusion and BD Facs Aria IIIu cell sorters in the Georgia Institute of Technology Cellular Analysis Core. The antibody clones used were the following: anti‐CD31 (390, BioLegend), anti‐CD45.2 (104, BioLegend), anti‐CD68 (FA11, Biolegend), anti‐CD3 (17A2, Biolegend), anti‐CD19 (6D5, Biolegend), anti‐CD11b (M1/70, Biolegend), anit‐CD11c (N418, Biolegend), anti‐CD4 (GK1.5, Biolegend), anti‐CD8a (53‐6.7, Biolegend), anti‐CD34 (SA376A4, Biolegend), anti‐CD25 (3C7, Biolegend), anti‐CD326 (G8.8, Biolegend), and PE anti‐mCD47 (miap301, BioLegend). Representative flow gates are located in Supplementary Figure 3. PBS‐injected Ai14 mice were used to gate tdTomato populations for intravenous administration.
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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

Quantitative GD2 CAR T-Cell Analysis

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GD2 CARs were detected with the 14g2a anti-idiotype antibody 1A7 (National Cancer Institute BRB Repository). Additional antibodies for flow cytometry include: anti-CD4 (GK1.5, BioLegend), anti-CD8a (53–6.7, BioLegend), anti-CD62 L (IM7, BioLegend), anti-CD44 (MEL-14, BioLegend), anti-GD2 (14G2a, BioLegend). Cells were washed with PBS containing 2% Bovine Serum Albumin before the addition of the antibody at a concentration of 0.2 µg per 1 × 106 cells in 100 µL volume. After 30 minutes of incubation with antibodies at 4°C in the dark, cells were washed once with PBS before being resuspended in PBS with 2% Bovine Serum Albumin (BSA). Quantitative flow cytometry was conducted using the QIFIKIT (Agilent, Santa Clara, CA). The GD2 primary antibody (14G2a, BioLegend) was added to 1 × 105 cells at a saturating dose (1 µg) and incubated at 4°C for 45 minutes. This was followed by washing and the addition of 0.5 µg of the secondary stain with APC-F(ab’)2-Goat anti-Mouse IgG (H + L) secondary antibody (Thermofisher) to samples and calibration beads. After a 30 minute incubation at 4°C, samples were washed and DAPI was added. All samples were analyzed with an LSR Fortessa or FACSAria II (BD Bioscience, San Jose, CA) and data were analyzed using FlowJo.
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5

Confocal Microscopy for Immune Cell Phenotyping

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Confocal microscopy was performed as described previously (26 (link)). Briefly, tissues were embedded in OCT medium (Tissue Tek) and 12 μm sections were cut using a cryostat. Sections were fixed and stained using the FoxP3 buffer set (eBiosciences) and directly conjugated antibodies. Sections were imaged on an Olympus confocal microscope with a 20x objective. For micrograph panels, single z slices were linearly contrasted and merged images were made in Adobe Photoshop. The following directly conjugated antibodies were used: anti-CD8a (53-6.7, BioLegend), anti-FoxP3 (FJK-16s, eBioscience), and anti-CD4 (RM4-5, BioLegend).
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6

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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7

Comprehensive Immune Cell Profiling

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Samples of tumor, spleen, lymph node, and blood were harvested after killing the mice. Single-cell suspensions of tumors were obtained using a Tumor Dissociation Kit (Miltenyi). The single cells were then incubated in MACS buffer (PBS supplemented with 2% FBS and 1 mM ethylenediaminetetraacetic acid [EDTA]) containing 10 µg/mL CD16/CD32 antibody (2.4G2, BD PharMingen) for 30 min at 4 °C and then stained with the antibodies. Staining reagents included anti-CD45 (30-F11, BioLegend), anti-CD45 (30-F11, BioLegend), anti-CD3 (17A2, BioLegend), anti-CD3 (17A2, BioLegend), anti-CD4 (RM4-5, BioLegend), anti-CD8a (53-6.7, BioLegend), anti-CD25 (PC61, BioLegend), anti-CD44 (IM7, BioLegend), and anti-CD62L (MEL-14, BioLegend). Data were collected on an BD FACSAria Fusion flow cytometer and analyzed with FlowJo software (TreeStar). Dead cells and cell aggregates were excluded from analyses based on a LIVE/DEAD Fixable Near-IR Dead Cell Stain Kit (eBioscience), or DAPI, with forward scatter/side scatter characteristics. The immune cell gating strategy was as follows: T cell: CD45+ CD3+, CD4+ T cell: CD45+ CD3+ CD4+, CD8+ T cell: CD45+ CD3+ CD8+, B cell: CD45+ CD3 CD19+.
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8

Multicolor Flow Cytometry of Immune Cells

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Fluorophore- or biotin-conjugated antibodies specific for mouse cell-surface antigens and cytokines were as follows: anti-B220 (RA3-6B2, BioLegend), anti-CD4 (GK1.5, BioLegend), anti-CD8a (53-6.7, BioLegend), anti-CD11b (M1/70, BioLegend), anti-Gr1 (RB6-8C5, BioLegend), anti-CD25 (3C7, BioLegend), anti-Foxp3 (MF14, eBioscience), anti-TER119 (TER-119, BioLegend), anti-CD71 (R17 217.1.3, BioXCell for depletion; C2F2, BD biosciences for FACS analysis), anti-CD45 (I3/2.3, BioLegend), anti-CD90.1 (16-10A1, BioLegend), anti-Gzmb (GL1, BioLegend), anti-IFN-γ (XMG1.2, BioLegend). anti-CXCR5 (L138D7, BioLegend), anti-mouse/human CD44 (IM7, BioLegend), anti-human/mouse Bcl-6 (7D1, BioLegend), anti-T-bet (4B10, BioLegend), anti-mouse Ki-67 (16A8, BioLegend), anti-mouse TNF-α (MP6-XT22, BD). For human studies, the following fluorophore- or biotin-conjugated antibodies specific for cell surface markers or cytokines were used: anti-CD3 (UCHT, BioLegend), anti-CD8 (PRA-T8, BioLegend), anti-CD45 (2D1, BioLegend), anti-CD71 (CY1G4, BioLegend), anti-CD235a (HI264, BioLegend). ROS production was measured by labelling with 2′,7′ –dichlorofluorescin diacetate using the ROS detection kit (S0033, Beyotime).
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9

Multiparameter Analysis of Immune Cells

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Tissues were excised from mice, minced and digested in Collagenase for 30 min. The samples were filtered through a 40-μm filter. Erythrocytes were removed with Lysing buffer (BD Biosciences). The samples were then incubated for 10 min with anti-CD16/CD32 blocking antibodies (BD Biosciences). The cells were stained with the following antibodies: anti-CD206 (C068C2, BioLegend), anti-CD11c (HL3, BD Biosciences), anti-CD11b (M1/70, BioLegend), anti-CD45 (30-F11, eBioscience), anti-F4/80 (CI: A3-1, BD Bioscience), anti-I-A/I-E (M5/114.15.2, BioLegend), anti-CD8a (53-6.7, BioLegend), anti-CD4 (GK1.5, BioLegend), anti-TCRβ (H57-597, BioLegend), anti-PD-1 (29F.1A12, BioLegend), and anti-CD44 (IM7, BioLegend). The samples were washed, incubated with 7-amino-actinomycin D (BD Biosciences) and then analysed on a FACSAria II (BD Biosciences).
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10

Multiparametric Flow Cytometry Analysis of Tumor-Infiltrating Immune Cells

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Anti-CD3 (17A2, cat. 561388), anti-CD4 (RM4-5, cat. 553047), anti-CD44 (IM7, cat. 561859), anti-CD62L (MEL-14, cat. 560516), anti-B220 (RA3-6B2, cat. 553091), anti-Foxp3 (MF23, cat. 562996) and anti-CD23 (B3B4, cat. 561772) were purchased from BD company (Franklin Lakes, NJ, USA). Anti-CD8a (53–6.7, cat. 100734), anti-IgM (RMM-1, cat. 406531) and anti-CD21 (7E9, cat. 123411) were obtained from BioLegend (San Diego, CA, USA). For flow cytometry experiments, total eight axillary LNs were dissected from four each of normal and tumor-bearing mice and pooled separately. Cells were harvested and washed with 1X PBS. Cells were stained with antibodies within 1:100 dilution for 40 min at 4°C with gentle mix, then washed with 1X PBS prior to Attune NxT cytometer (Thermo Fisher Scientific) analysis. For Foxp3 staining, cells were mixed with 1 ml of Fix/Perm solution and incubated at room temperature for 15 min. Cells were washed with 1X PBS and stained with anti-Foxp3 antibody for flow cytometry analysis.
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