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24 protocols using anti cd4 rm4 5

1

Naive T cell differentiation conditions

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Naive CD4+ T cells were purified from dissociated spleens and lymph nodes of C56BL/6N mice by fluorescence-associated cell sorting (FACS) (CD4+CD62LhiCD44lo). Purified cells were cultured under TH0 condition stimulated with anti-CD3e (5 μg/mL, clone 145– 2C11, eBioscience), anti-CD28 (5 μg/mL, clone 37.51, eBioscience), and human IL-2 (100 U/mL, Peprotech). Additional TGFβ (0.25 ng/mL, Peprotech) was added for Treg polarization conditions. Bile acids, retinoic acid (1 nM, Sigma), or mitoParaquat (5 μM, Sigma) were added on day 0. IsoalloLCA dissolved in DMSO was resuspended in culture media and sonicated before being added to the culture. Cells were harvested either at 48 hours for RNA-Seq, ATAC-Seq, ChIP analysis, or at 72 hours followed by staining with anti-CD4 (RM4–5, eBioscience) or anti-Foxp3 (FJK-16s, eBioscience) antibodies, and analyzed with LSR II flow cytometer (BD). For mitoROS detection, cells cultured for 48 hours were incubated with 5 μM mitoSOX (ThermoFisher) for 30 min and assayed by flow cytometry. Flow cytometry data were acquired on an LSR II flow cytometer or Symphony flow cytometer (both BD) and data were analyzed with FlowJo software (TreeStar).
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2

Comprehensive Immune Cell Analysis

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Spleens were collected and single cell suspensions made. For T helper cell analysis, cells were surfaced stained with anti-CD4 (RM 4-5; eBioscience), permiabalized and intracellular stained with IFN-γ (XMG1.2; eBioscience), IL-4 (BVD6-24G2; eBioscience), RORγ (B2D; eBioscience), CD25 (PC61.5; eBioscience) or FoxP3 (FJK-16s; eBioscience). Representative gating in Supplemental Data Figure S1. For CD8+ T cells, cell surfaces were stained with anti- CD8a (53-6.7; eBioscience) and anti- CD3e (145-2C11; eBioscience). For B cells, cell surfaces were stained with anti- CD21/CD35 (8D9; eBioscience) and anti- CD19 (1D3; eBioscience). T cell activation markers CD25 (eBio3C7; eBioscience) and CD69 (H1.2F3, Biolegend) were measured using flow cytometry.
For CBC exams ≈ 50 μL of blood was collected into EDTA coated tubes via retro-orbital bleed. VetScan HM5 Analyzer was used.
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3

Thymic Epithelial Cell Immunophenotyping

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Thymic epithelial cells were acquired as described above. Cells were incubated with 2.4G2 before staining with other antibodies. The antibodies used included anti-CD45 (30-F11, eBioscience), anti-EpCAM (G8.8, Biolegend), anti-Ly51 (6C3, Biolegend), FITC labelled Ulex europaeus agglutinin-1 (UEA-1; Vector Laboratory), anti-IA/IE (M5/114.15.2, Biolegend), anti-SSEA-1 (MC-480, Biolegend), anti-LTβR (eBio3C8, eBioscience). C-CPE (C. perfringens enterotoxin) was produced as described47 (link) and biotin-conjugated; Streptavidin APC-eFluor 780 (eBioscience) was used for visualization of C-CPE. For intracellular staining of Ki-67 (B56, BD) and active caspase 3 (C92-605, BD), cells were fixed and permeabilzated with BD Cytofix/Cytoperm™ Fixation/Permeabilization Solution Kit (554714) and stained according to the manufacture’s protocols. Fixable viability dye (L-34967, ThermoFisher) was used to exclude dead cells. For thymocyte and splenocyte analysis, cells were stained with anti-CD4 (RM4-5, eBioscience), anti-CD8 (53-6.7, eBioscience), anti-Va2 (B20.1, eBioscience), anti-Vb5 (MR9-4, eBioscience), and anti-CD24 (M1/69, Biolegend) before flow cytometry analysis. The samples were analyzed on BD LSRFortessa and FlowJo software (Tree Star Inc).
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4

Phenotyping of Dendritic Cells by FACS

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After homogenizing spleens, cells were treated with erythrocyte lysis buffer, meshed through a 35-μm cell strainer, washed with PBS, and analyzed by FACS.
DCs were phenotyped by using fluorochrome-labeled mAbs directed against CD11c (N418; BioLegend), CD80 (16-10A1; BD Pharmingen, Heidelberg, Germany), CD86 (PO3; Thermo Fisher Scientific), PD-1 (J43, Thermo Fisher Scientific), CTLA-4 (UC10-4B9; BioLegend), CD83 (Michel-19; BioLegend), CD40 (3/23; BioLegend), MHCII (2G9; BD Pharmingen) and PD-L1 (MIH6; AbD Serotec, Puchheim, Germany). Dead cells were excluded using the LIVE/DEAD™ Fixable Blue Dead Cell Stain Kit (Thermo Fisher Scientific). Following mAb labeling for 30 min at 4 °C and final washing, cells were analyzed on an LSR II flow cytometer.
To measure intracellular cytokines, cells were stimulated with PMA and ionomycin (1 μg/ml each; Sigma-Aldrich, Taufkirchen, Germany) for 4 h in the presence of 3 μg/ml Brefeldin A (Thermo Fisher Scientific), labeled for CD11c, subjected to fixation and permeabilization and subsequently stained with mAbs against IL-10 (JES5-16E3; BD Pharmingen) and IL-12 (C15.6; BD Pharmingen). IFN-γ in T cells was measured by using fluorochrome-labeled anti-IFN-γ (XMG-1.2, BioLegend) and counterstaining with anti-CD4 (RM4-5, eBioscience, Frankfurt, Germany).
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5

Isolation and Activation of Murine Naive CD4+ T Cells

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Naive CD4+ T cells were purified from the dissociated spleens and lymph nodes of C57BL/6N mice by fluorescence-associated cell sorting (FACS) (CD4+CD62LhiCD44lo 572). Purified cells were cultured under TH0 condition stimulated with anti-CD3e (5 μg/mL, clone 145– 2C11, eBioscience), anti-CD28 (5 μg/mL, clone 37.51, eBioscience), and human IL-2 (100 U/mL, Peprotech). Bile acids were added on day 0. IsoalloLCA dissolved in DMSO was resuspended in culture media and sonicated before being added to the culture. Cells were harvested at 72 hours followed by staining with anti-CD4 (RM4–5, eBioscience) or anti-Foxp3 (FJK-16s, 580 eBioscience) antibodies, and analyzed with LSR II flow cytometer (BD).
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6

Immunophenotyping of Murine Splenocytes and Thymocytes

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Mouse splenocytes and thymocytes were prepared from pooled thymus or spleen. Thymic and splenic cells were pre-incubated with Fc-block before staining with other antibodies. The mouse antibodies used included anti-CD4 (RM4–5, eBioscience); anti-CD8 (53–6.7, eBioscience); anti-CD45.1 (A20, BioLegend), anti-CD45.2 (104, eBioscience); anti-CD25 (PC61.5, eBioscience); anti-CD69 (H1.2F3, eBioscience); anti-CD24 (M1/69, eBioscience); anti-Helios (22F6, eBioscience) before flow cytometry analysis. For intracellular staining of Ki-67 (B56, BD), pSTAT5 (47/Stat5(pY694), BD) and Foxp3 (NRRF-30, eBioscience), cells were fixed and permeabilized with BD Cytofix/Cytoperm™ Fixation / Permeabilization Solution Kit (554,714, BD) and stained according to the manufacturer’s protocols. The CD4+ T cells from the thymus and spleen of WT or RelB−/− mice were analyzed by flow cytometry and gated as shown in the Supplementary Figure 1. The samples were analyzed using a BD LSRFortessa flow cytometer and FlowJo software (Tree Star Inc). All single-cell suspensions from the tissues were stained with Abs diluted in PBS containing 2% FCS for 30 min on ice.
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7

Immunohistochemical Analysis of Lymphoid Tissues

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dLN and spleen were harvested into PLP buffer (0.05 M phosphate buffer containing 0.2 mL lysine (pH 7.4), 2 mg ml−1 NaIO4, 10 mg ml−1 paraformaldehyde), fixed overnight and dehydrated in 30% sucrose prior to embedding in OCT freezing media (Sakura Fineteck). Frozen sections (10 µm) were cut on a CM1950 Cryostat. Sections were stained in PBS (0.01% Triton X-100 and 5% goat serum) using the following Abs: anti-B220 (RA3-6B2, 1:200, eBioscience) and anti-CD4 (RM4-5, 1:200, eBioscience), CD45.1 (A20, 1:100, BD Biosciences). Images were acquired on a Apotome ZEISS Inv. Regions and cells were defined with IMARIS image analysis software.
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8

Isolation of Murine Brain Leukocytes

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Mice were euthanized by isoflorane overdose to keep their circulatory system intact. Mice were perfused with 30mls of 1X PBS. Brain was collected in 2mls RPMI+5%FBS. Brain was disassociated over a 40μm strainer using the plunger of a 3ml syringe. The strainer was washed well with 15-25mls of RPMI+5%FBS. The suspension was centrifuged at 1650 RPM, 5 mins, 4°C and the pellet resuspended in 7mls of 30% Percol in a 15ml conical tube, centrifuged at 1650 RPM, 30 mins at room temperature or 4°C. Myelin and excess percol was aspirated off and the pellet was transferred to a new 15ml conical tube and washed with 10mls of RPMI+5%FBS followed by centrifugation at 2000 RPM, 5 mins, 4°C. The pellet was then transferred in a 96 well microtitre plate for surface staining [LIVE/DEAD yellow (Life Technologies, Carlsbad, CA), anti-CD3 (2c11, eBiosciences), anti-CD4 (RM4-5, eBiosciences), anti-CD8α (53–6.7, eBiosciences), E641:I-Ab tetramer].
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9

Immunofluorescent Staining of Ear Pinnae

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Ear pinnae were split with forceps, fixed in 1% paraformaldehyde (Electron Microscopy Sciences) overnight at 4°C, and blocked in PBS containing 1% BSA and 0.25% Triton X-100 for 2 h at room temperature. Tissues were first stained with anti-CD4 (RM4–5, eBioscience), anti-CD8α (53–6.7, eBioscience), anti-CD49f (GoH3, eBioscience), anti-GFP (A21311, Life Technologies), and anti-TCRβ (H57–597, eBioscience) antibodies overnight at 4°C, washed three times with PBS, and then stained with DAPI (Sigma-Aldrich) overnight before being mounted with ProLong Gold (Invitrogen). Ear pinnae images were captured on a Leica TCS SP8 confocal microscope equipped with HyD and PMT detectors and a 40X oil objective (HC PL APO 40X/1.3 oil). Images were analyzed using Imaris (Bitplane).
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10

Multiparametric Flow Cytometry Analysis

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Cell staining was performed using the following monoclonal antibodies: anti-CD4 (RM4-5; eBioscience), anti-CD25 (PC61.5; eBioscience), anti-CD44 (IM7; BioLegend), and anti-CD62L (MEL-14; BioLegend). For intracellular staining, cells were first re-stimulated with a cell stimulation cocktail (00-4975-03; eBioscience) for 4 h at 37°C, after which staining of cell surface markers was performed. After staining of the surface markers, the cells were fixed and permeabilized. Intracellular staining was performed using the following monoclonal antibodies: anti-IL-17A (eBio17B7; eBioscience), anti-IFN-γ (XMG1.2; eBioscience), anti-IL-4 (11B11; BioLegend), anti-IL-13 (eBio13A; eBioscience), and anti-Foxp3 (FJK-16s; eBioscience). Stained cells were detected by flow cytometry (FACSCanto II; BD Biosciences), and data were analyzed using FlowJo software version 10.0.7 (Tree Star).
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