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1

Comprehensive Flow Cytometry Panel for Mouse T Cells

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Flow cytometry monoclonal antibodies against mouse antigens (CD4, clone RM4-5; CD8a, clone 53–6.7; CD62L, clone MEL-14; IFN-γ, clone XMG1.2; IL-2, clone JES6-16E3; Ifnar1, clone MAR1-5A3; PD-1, clone RMP1-30; T-bet, clone 4B10) were obtained from Biolegend. Tim-3 monoclonal antibody (clone 5D12) was a gift from V. Kuchroo. Carboxyfluorescein succinimidyl ester (CFSE) was obtained from Biolegend. The following recombinant cytokines and antibodies were used for in vitro T cell cultures: mIFN-β (PBL InterferonSource, indicated concentrations), mIL-12 (R&D Biosystems, 10 ng mL-1), mIL-2 (Miltenyi, 5 ng mL-1), hTGF-β (Miltenyi, 3 ng mL-1), mIL-6 (Miltenyi, 20 ng mL-1), mIL-23 (R&D Biosystems, 20 ng mL-1), anti-mIL-4 (BioXCell; clone 11B11, 10 μg mL-1), anti-CD3 (eBioscience; Functional Grade Purified, clone 145-2C11, 2 μg mL-1), anti-CD28 (Biolegend; LEAF-purified, clone 37.51, 2 μg mL-1). Western blotting primary antibodies were obtained from BD Transduction Laboratories (Stat1, clone 42/Stat1, dilution 1:1000; Stat1 pY701, clone 14/P-STAT1, dilution 1:1000; Stat4 pY693, clone 42/Stat1, dilution 1:500), Cell Signaling (Stat4, clone C46B10, dilution 1:500) or Millipore (GAPDH, mAb374, dilution 1:1000). Anti-mouse or-rabbit secondary antibodies were obtained from Jackson Immunoresearch and were used at 1:10000.
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2

Purified CD4+ T Cell Differentiation

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Purified CD4+ T cells were prepared using immunomagnetic negative selection (Miltenyi Biotec). Briefly, lymphocytes were allowed to react with CD4+ T cell biotin-antibody cocktail (biotin-conjugated monoclonal antibodies against CD8a, CD11b, CD11c, CD19, CD45R (B220), CD49b (DX5), CD105, anti-MHC class II, Ter-119, and TCRγ/δ) and then incubated with antibiotin microbeads, followed by magnetic separation. The purity of the resulting CD4+ T cell populations was examined using flow cytometry, and was consistently above 95%.
T-helper cell differentiation was conducted as previously described [26 (link)]. Briefly, naive CD4 T cells (0.4 × 106) in 24-well plates (Costar) precoated with 5 μg/ml of anti-CD3 (154-2C11, BioXcell) and 2 μg/ml of anti-CD28 (37.51, BioXcell) were cultured in RPMI containing 10% FCS and polarizing cytokines at the various concentrations of ECF. The cytokines used were Th1, mIL-12 (10 ng/ml, Biolegend), and anti-mIL-4 (11B11, 2 μg/ml, BioXcell). Cells stimulated in “neutral” conditions (anti-mIL-4 and anti-mIFN-γ without cytokines) were considered Th0 cells. The differentiated cells were harvested after 3 days and restimulated for 4 h with 50 ng/ml of PMA (Sigma-Aldrich) and 750 ng/ml of ionomycin (Sigma-Aldrich) in the presence or absence of Brefeldin A for flow cytometry.
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3

Mouse CD4+ T Cell Differentiation Protocol

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A mouse CD4+ T cell isolation kit (Miltenyi Biotec or BioLegend) was used to isolate CD4+ T cells from LN and spleen. The isolated CD4+ T cells were stimulated for 3 d with plate-bound anti-hamster IgG (12.5 µg/ml), soluble anti-CD3ɛ (145-2C11; BD PharMingen), and anti-CD28 (37.51; BD PharMingen). On day 2, cells were transferred to a fresh plate, without or with the addition of 75 U/ml hIL-2 (Peprotech) and 10 µg/ml anti–mIL-2 (Bio X Cell). The culture conditions for Th0 (no differentiation) were 2.5 µg ConA; for Th1, Th2, and iT reg, 0.5 µg/ml anti-CD3 and 1 µg/ml anti-CD28; and for Th17, 0.25 µg/ml anti-CD3 and 1 µg/ml anti-CD28. For skewing, the following cytokines were added to the culture: Th0, 2.5 µg/ml anti–mIL-4 (Bio X Cell) and 2.5 µg/ml anti–mIFN-γ (Bio X Cell); Th1, 10 ng/ml mIL-12 (PeproTech) and 2.5 µg/ml anti–mIL-4; Th2, 50 ng/ml mIL-4 (PeproTech) and 2.5 µg/ml anti–mIFN-γ; Th17, 0.5 ng/ml mTGFβ, 20 ng/ml mIL-6 (both Peprotech), 2.5 µg/ml anti–mIFN-γ, and 2.5 µg/ml anti–mIL-4; and iT reg, 5 ng/ml mTGFβ, 5 µg/ml anti–mIFN-γ, and 5 µg/ml anti–mIL-4. The cell culture medium was RPMI 1640 for Th1, Th2, and iT reg or IMDM for Th17 cell differentiation and supplemented with 5% FCS, β-mercaptoethanol, and penicillin/streptomycin (Invitrogen).
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Polarized CD4+ T Cell Differentiation

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Naive CD4 T cells (0.4 × 106) in 24 well plates (Costar) pre-coated with anti-CD3 (154-2C11, 5 μg/ml, BioXcell) and anti-CD28 (37.51, 2 μg/ml, BioXcell) were cultured in RPMI containing 10% FCS and polarizing cytokines. The cytokines were: Th1, mIL-12 (10 ng/ml, Biolegend) and anti-mIL-4 (11B11, 2 μg/ml, BioXcell); Treg, hTGF-β1 (3 ng/ml, Biolegend), mIL-2 (20 ng/ml, Biolegend), anti-mIFN-γ (XMG1.2, 2 μg/ml, BioXcell) and anti-mIL-4; Th17, mIL-6 (10 ng/ml, Biolegend), hTGF-β1 (2 ng/ml), anti-mIFN-γ, and anti-mIL-4. Cells stimulated in ‘neutral’ conditions (anti-mIL-4 plus anti-mIFN-γ without added cytokines) were considered Th0 cells.
Where studied, protease inhibitors, AEBSF (Pefabloc) and E64 (Sigma-Aldrich), E64D (Santa Cruz), z-Phe-Ala-fmk (Enzyme Systems), CA074-OMe (EMD Millipore), Ns-Ile-Trp-CHO (IW-CHO, Enzo Life Sciences), CLIK195 (provided by Guo-Ping Shi), and the AEP inhibitor LI-1 [15 (link)], were added at the start of culture. Unless otherwise indicated, differentiated cells were harvested after 3 days for Western blot, peptidase assay or active site labeling or were restimulated for 4h with PMA (50 ng/ml) and ionomycin (750 ng/ml) (Sigma-Aldrich) in the presence or absence of Brefeldin A for flow cytometry or ELISA, respectively.
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