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8 protocols using recombinant tnf

1

Antibody and Chemical Sources for Cell Signaling

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The antibodies and chemicals were obtained from the following resources; anti-PARP (#556362), anti-XIAP (#610716), anti-FADD (#610399), anti-RIP1 (#610459), anti-p53 (#554147) and anti-p21 (#556430) antibodies (BD Biosciences, San Diego, CA, USA); anti-caspase-3 (#9662), anti-caspase-8 (#9746), anti-caspase-9 (#9508) and anti-Bid (#2002) antibodies (Cell signalling Technology, Beverly, MA, USA); anti-caspase-10 (M059-3) antibody (MBL, WOBURN, MA, USA); anti-Bcl-XS/L (sc-271121), anti-survivin (sc-17779), anti-TRAF2 (sc-876), anti-GFP (sc-9996) and anti-HA (sc-805) antibodies (Santa Cruz, CA, USA); anti-c-FLIP (ALX-804-961) antibody (Enzo Life Sciences, Farmingdale, NY, USA); anti-cIAP1/2 (#07-759) antibody (Upstate Biotech, Waltham, MA, USA); anti-DR5 (#ab181846) antibody (Abcam, Cambridge, UK); anti-DR4 (NB100-56528) antibody (Novus, Centennial, CO, USA); anti-TurboGFP (PA5-22688) antibody (Thermo scientific, Waltham, Massachusetts, USA); anti-actin (A2066), anti-flag (F3165, 1:2,000 dilution) antibodies (Sigma-Aldrich, St. Louis, MO, USA). the pan caspase inhibitor Z-VAD-FMK, MG-132, TPCA-1 (Calbiochem, San Diego, CA, USA); recombinant TNF (R & D Systems, Minneapolis, MN, USA); recombinant human TRAIL/Apo2 ligand (Peprotech, Rocky Hill, NJ, USA).
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2

Enhancer Activation Assay for Sox4, Sox11, Il15, Mapk1

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ChIP-seq enhancer peak regions assigned to Sox4, Sox11, Il15 and Mapk1 were amplified from mouse genomic DNA and cloned into pBV- Luc, a luciferase reporter plasmid with a minimal promoter and very low basal activity (24 (link)). These reporter plasmids were co-transfected with 3X-FLAG SOX4 or 3X-FLAG SOX11 expression plasmids (14 (link)) into HEK293 cells using Viromer Red reagent (Origene). pSV2bgal plasmid was used as a control for transfection efficiency. Cells were treated with 10ng/mL recombinant TNF (R&D systems) for the last 16h of the 36h transfection period. Luciferase and β-galactosidase activities were assayed using the Dual-light combined reporter gene assay system (Applied Biosystems) using Synergy H1 Multi-Mode Plate Reader (Biotek). Reporter activities were normalized for transfection efficiency and reported as fold change in luciferase activity. Assays were performed as triplicates.
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3

PBMC Isolation and Stimulation Assay

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Peripheral blood mononuclear cells (PBMC) were isolated from heparinized venous blood by Ficoll-Hypaque (GE Healthcare Bio-Sciences AB, Sweden) gradient centrifugation. After washing three times in 0.9% NaCl, PBMC were adjusted to 3×106 cells/ml in 1 ml of RPMI-1640 (Gibco Laboratories, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (FBS) (Gibco Laboratories, South America Invitrogen), 10 IU/ml penicillin and 100 µg/ml streptomycin. Cells were placed on 24 wells plates and incubated for 24 or 72 hours in the presence or absence of SLA (5 µg/ml) or recombinant TNF (5 ng/ml), or anti-TNF antibody (10 µg/ml) (R&D systems, Minneapolis, MN), as indicated in figures.
Biopsies from L. braziliensis patients and HS were cultured in complete RPMI media without stimuli. Tissue from CL patients and HS were cultured in RPMI for 12 hours. Supernatants from PBMC and biopsies were collected and stored at −70°C. The Levels of MMP-9, TIMP-1 (BD Biosciences, San Diego, CA, USA) and TNF (R&D Systems, Minneapolis, MN) were measured by ELISA according to the manufactures instructions. The results are expressed in pg/ml.
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4

Western Blot Analysis of Apoptosis Signaling

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Cells for Western blot analysis were lysed in Lämmli Buffer (Bio-Rad, Hercules, CA, USA) with protease inhibitors (Thermo Fisher, Waltham, MA, USA) and sodium orthovanadate (Sigma Aldrich, St. Louis, MO, USA) according to the manufacturer’s protocol. Thirty micrograms of total protein were separated on ExcelGels (GE Healthcare) and transferred onto nitrocellulose membranes (Bio-Rad). After blocking, membranes were incubated with primary antibodies [cleaved caspase-3 antibody (0.5 µg/ml, #MAB835; R&D Systems, Minneapolis, MN, USA), phospho-RIPKs 1 (1:100, #65746; Cell Signalling Technology, Cambridge, UK), phospho-RIPK3 (1:200, #ab209384; Abcam, Cambridge, UK), phospho-MLKL (1:500, #91689; Cell Signalling Technology, Cambridge, UK), or glyceraldehyde 3-phosphate dehydrogenase (1:2000, #2118; Cell Signalling Technology, TNF (1 µg/ml, R&D Systems)] overnight at 4 °C. After further incubation with horseradish-conjugated goat-anti-rabbit antibody (1:10,000, #170-6515; Bio-Rad, Hercules, CA, USA), secondary antibodies were visualized with Supersignal West Dura (Thermo Fisher, Waltham, MA, USA) and signals were detected using ChemiDoc System (Bio-Rad). For blocking of the TNF antibody, 1 µg TNF antibody was pre-incubated with 10 µg recombinant TNF (R&D Systems) for 4 h at 4 °C:
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5

Modulating Type I IFN and TNF Signaling in CD4+ T Cells

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For type I IFN neutralization experiments, a cocktail of 3 µg/ml B18R (eBioscience), 2.5 µg/ml anti–IFN-β (eBioscience), 1.2 µg/ml anti–IFN-α (eBioscience), and 0.6 µg/ml anti-IFNAR (EMD Millipore) was added at the time of CD4+ T cell transduction. Reverse transcription inhibitors azidothymidine (25 µM) and nevirapine (10 µM) were used to inhibit lentiviral transduction as a negative control. To inhibit caspases, 50 µM Z-VAD-FMK (R&D Systems) was added at the time of transduction and maintained during the course of the experiment. 25 µM etoposide (Sigma-Aldrich) was added for 24 h at day 3 after transduction. For TNF neutralization experiments, a cocktail of 10 µg/ml anti–human TNFRI (R&D Systems), 10 µg/ml anti–human TNFRII (R&D Systems), and 10 µg/ml anti–human TNF (R&D Systems) was added at the time of CD4+ T cell transduction and maintained during the course of the experiment. Recombinant TNF (R&D Systems) was added to CD4+ T cells transduced with NF-κB reporter lentivector 24 h before analysis.
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6

Recombinant TNF and suPAR Experiments

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Recombinant TNF was obtained from R&D Systems (Minneapolis, MN). A large recombinant form of suPAR containing domains 1, 2 and 3 was also obtained from R&D Systems. A smaller recombinant form of suPAR containing domains 2 and 3 provided by Dr. Sanja Sever of the Harvard Medical School (Boston, MA) was used in a few experiments. SKF-96365 was obtained from Sigma Aldrich (St. Louis, MO), and cilengitide was obtained from Seleck Chem (Houston, TX, USA). ELISA assay kits for quantifying serum TNF (DTA00C) and suPAR (DUP00) were obtained from R&D Systems. Antibodies used for neutralization of suPAR (AF-807) and TNF (AF-210-NA) in a nephrotic plasma sample were from R&D Systems.
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7

Investigating TGFβ-Mediated Immune Regulation

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Splenocytes isolated from OT-I.CD901.1XIKK2CAfl/fl xGzBCre mice were stimulated with 20 nM OVA peptide for 48 h at a concentration of 1 × 106 cells/ml. TGFβ (R&D Systems, Minneapolis, MN) was then added to a final concentration of 50 ng/ml. At 30 min and 24 h post TGFβ stimulation, cells were harvested for analysis by flow cytometry and western blotting. Splenocytes from CD2rtTA x DN-IKK2 mice were stimulated in vitro at 1 × 106 cells/ml with 10 μg/ml anti-CD3 (clone 145-2C11) and 10 μg/ml anti-CD28 (clone 37.51) (ThermoFisher Scientific, Waltham, MA). Following 24 h of stimulation, cells were divided and incubated in the presence or absence of 125 ng/ml recombinant TNF (R&D Systems, Minneapolis, MN) for 24 additional hours. The cells were again divided and incubated in the presence or absence of 50 ng/ml TGFβ (R&D Systems, Minneapolis, MN). Cells were harvested at 30 min and 24 h post addition of TGFβ and analyzed by flow cytometry.
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8

Thymocyte Culture and NF-κB Activation

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Thymocytes were cultured at 37°C with 5% CO2 in RPMI-1640 (Invitrogen) supplemented with 10% (vol/vol) FBS (Invitrogen), 0.1% (vol/vol) 2-mercaptoethanol βME (Sigma-Aldrich), and 1% (vol/vol) penicillin-streptomycin (Invitrogen; RPMI-10). Recombinant TNF, BAFF, LIGHT, APRIL, TRAIL, GITRL, CD70, and TLA1 were supplemented to cultures at 100 ng/ml unless otherwise state, and were obtained from R&D Systems, with PBS used as vehicle. IKK2 inhibitor Bl605906 was used at 10 µM in DMSO vehicle. Binding of RelA from nuclear extracts of TNF-stimulated thymocytes to NF-κB oligonucleotide was determined by specific ELISA (Active Motif) according to the manufacturer’s instructions.
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