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12 protocols using tnf α 300 01a

1

Molecular Signaling Modulators in Inflammation

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Interferon-gamma (IFN-γ, 300-02) and tumor necrosis factor alpha (TNF-α, 300-01A) were purchased from Peprotech. AMPK agonists Metformin hydrochloride (PHR1084), AICAR (A9978), Resveratrol (R5010); SIRT1 agonist SRT1720 (SRT1720) and NRF-2/HO-1 agonist Protoporphyrin IX cobalt chloride (C1900) were purchased from Sigma-Aldrich. Inhibitors of NF-κB Emodin (E7881) and JSH23 (J4455); IKKβ inhibitor IKK16 (SML1138); STAT1 inhibitor Fludarabine (F2773) and NOS2 inhibitor 1400W (W4262) were purchased from Sigma-Aldrich. Inhibitors of MEK1 and MEK2 PD98059 (ab120234), JNK SP600125 (ab120065) and MAPK SB202190 (ab120638) were purchased from Abcam. Reagents were dissolved in DMSO or water (Metformin and AICAR) at 100x stock concentrations and maximum DMSO concentration used in cells was 1%. Monoclonal antibody against 3-nitrotyrosine (ab61392) was purchased from Abcam. Monoclonal antibody against NF-κB p65 (sc-8008) was purchased from Santa Cruz Biotechnology.
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2

Monocyte-Derived Dendritic Cell Protocols

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Mature dendritic cells were differentiated from blood monocytes as previously described (Bruger et al, 2020 (link)). Briefly, monocytes (isolated from mononuclear cells of non-cancerous patients as described above) were resuspended in RPMI-1640 complemented with 10% FCS (Sigma-Aldrich), 200 nM L-alanyl-L-glutamine dipeptide (35050-038, GlutaMAX; Gibco), 100 U/ml penicillin + 100 μg/ml streptomycin (P4333; Sigma-Aldrich), 100 ng/ml of clinical grade GM-CSF (NDC0024-5843-05, Leukine [Sargramostim]; Sanofi-Aventis), and 30 ng/ml (5 × 105 U/ml) IL-4 (in-house) (DC medium). Monocytes were seeded in a 12-well tissue culture plate at 106 cells/well, and incubated for 5 d at 37°C and 5% CO2. Dendritic cells were matured at Day 5 with 50 μg/ml Poly-IC (P1530; Sigma-Aldrich) and 10 ng/ml TNF-α (300-01A; PeproTech) in DC medium for another 2 d at 37°C and 5% CO2. Cells were harvested at Day 7 and checked by flow cytometry to confirm their phenotype (CD3, CD19, CD14, CD11c+, CD1a+, CD83+) (see antibodies for flow cytometry). Mature DC were frozen at −80°C in 50% RPMI-1640, 40% FCS, and 10% DMSO for later use.
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3

Immune Signaling Pathway Modulation

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Pam3CSK4 (tlrl-pms), Poly(I:C) (tlrl-piclv), LPS (tlrl-peklps) and Flagellin (tlrl-pafla) were purchased from Invivogen. TNF-α (300–01A), IFN-γ (300–02) and IL-1α (200–01A) were purchased from Peprotech. HMGB1 (1690-HMB) was from R&D system. Rapamycin (S1039), Torin-1 (S2827), z-DEVD-FMK (S7312), z-VAD-FMK (S7023), GSK’872 (S8465) and ATP (S5260) were purchased from Selleck. Ac-YVAD-CMK (SML0429) and necrosulfonamide (480,073) were purchased from Sigma.
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4

Molecular Mechanisms of Endothelial Cell Regulation

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Actinomycin D (ActD) was purchased from Sigma-Aldrich (St. Louis, USA). Lipofectamine 2000 (11668–027) and Opti-MEM I reduced serum medium were obtained from Invitrogen (Carlsbad, USA). MK2 siRNA, HuR siRNA and negative control siRNA were received from GenePharma (Shanghai, China). TNF-α (300-01A) was purchased from PeproTech (Rocky Hill, USA). Phosphatase Inhibitor Cocktail (04906845001) was from Roche (Mannheim, Germany). An enhanced chemiluminescent (ECL) kit were obtained from Pierce (Rockford, USA). The protein assay kit, nuclear and cytoplasmic protein extraction kit (P0027) and the RIPA Lysis Buffer (P0013C) were purchased from Beyotime Institute of Biotechnology (Nantong, China). Antibodies raised against MK2 (#3042), phospho-MK2 (Thr334, #3041), ICAM-1 (#4915) was obtained from Cell Signaling (Danvers, USA); a monoclonal antibody against HuR (ab14371) was received from Abcam (Cambridge, USA); antibodies against β-actin (P30002) and histone (P30266) were from Abmart (Shanghai, China);IL-8 ELISA Kit (BMS204/3) was received from eBioscience (San Diego, USA). RevertAid First Strand cDNA Synthesis Kit (#K1622) was purchased from Fermentas UAB (Vilnius, Lithuania). FastStart Universal SYBR Green Master (Rox) (04913914001) was purchased from Roche (Mannheim, Germany). Endothelial cell medium and HPMECs were purchased from ScienCell (Carlsbad, USA).
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5

Multiplex Cytokine Assay Reagents

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Antibodies used in the study were purchased from R&D systems, including monoclonal capture antibodies: IL-1β (MAB601), IL-3 (MAB603R), IL-6 (MAB206), IL-10 (MAB2172), TNF-α (MAB610) and MCP-1 (MAB679); biotinylated polyclonal detection antibodies: IL-1β (BAF201), IL-3 (BAF203), IL-6 (BAF206), IL-10 (BAF217), TNF-α (BAF210) and MCP-1 (BAF279). Respective recombinant human proteins for spiking experiments were purchased from Peprotech: IL-1β (200-01B), IL-3 (200-03), IL-6 (200-06), IL-10 (200-10), TNF-α (300-01A) and MCP-1 (300-04).
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6

Dual Luciferase Reporter Assay in HEK293T Cells

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HEK293T cells were seeded at a density of 5 x 104 cells per well in 24-well plates overnight. Cells were then transfected with the experimental reporter plasmid pNF-κB-Luc (Firefly luciferase, Clontech, Mountain View, CA, USA), pIL8-Luc and the internal control plasmid pRL-TK (Renilla luciferase, Clontech), as well as other plasmids as described in the figure legend and our previous study.42 (link) When appropriate, cells were treated with PMA (79346, MilliporeSigma), TNF-α (300-01A, PeproTech) or IL-1β (200-01B, PeproTech). Enzyme activity was measured using the Dual Luciferase reporter assay kit (E1910, Promega) according to the manufacturer’s instructions.
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7

NFκB Transcriptional Regulation Assay

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Ovcar3 and Ovcar8 cells subjected to scrambled or Caspase 8 shRNA knockdown were first selected with puromycin as described before4 (link). After selection, cells were transduced with a lentiviral vector containing an NFκB transcriptional regulatory element, using the Cignal Lenti Reporter System (CLS-013L), according to the manufacturer’s specifications and allowed 72 h for maximum vector expression. Transient reporter assays were subsequently performed for 18 h. Briefly, cells were plated in 96-well plates at a density of 10,000 cells/well. After overnight attachment, cells were exposed to serum starvation medium containing 0.5% fetal bovine serum for 24 h. Drugs or IKKβ inhibitor IV (EMD Biosciences) were added for 1 h after which TNFα (300-01A, PeproTech) was added to stimulate NFκB activity for 18 h. Control wells received vehicle alone. Luciferase activity was measured using the Luciferase Assay System (E4030, Promega) according to the manufacturer’s instructions and a Spectramax M5 plate reader (Molecular Devices). Luciferase units were normalized to viable cell number, obtained by XTT assay, on duplicate assay plates. Experiments included 3–6 replicate samples per point and were repeated at least three times.
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8

Molecular Signaling Assays with Diverse Reagents

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LPS (L6529), puromycin (P8833), and PMA (P8139) were purchased from Sigma-Aldrich. TNF-α (300-01A) and IL-1β (200-01B) were from Peprotech. Cell lysis buffer (9803) was from Cell Signaling. Phosphatase Inhibitor Cocktail 3 (P0044) and Protease inhibitor cocktail (P8340) were from Sigma-Aldrich. Dynabeads Protein G (10004D), Dynabeads Protein A (10001D), SuperSignal West Femto Maximum Sensitivity Substrate (34096), and Pierce BCA Protein Assay (23225) were from Thermo Fisher Scientific. Dual-Luciferase Reporter Assay System (E1910) was from Promega. Nitrocellulose membrane (1620115) was from Bio-Rad. Polyethyleneimine (PEI) (24313-2) was purchased from Polysciences. Purified recombinant IKKα (TP761707) and IKKβ (TP750220) were purchased from Origene.
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9

TNFα-Induced Apoptosis Pathway Analysis

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TNFα (210-TA) (for in vivo experiments) was from R&D system; D-GalN (101743) was from Millipore; ConA, CHX, puromycin and doxycycline (DOX) were from Sigma Aldrich; ZVAD-FMK (s7023) and sp600125 (s1406) were from Selleck; LCL161 (HY-15518) was from MCE; TNFα (300-01 A) (for in vitro experiments) was from Peprotech; Flag-TNF was from Enzo Life (ALX-522-009-C050); Lipofectamine 2000 Transfection Reagent was from Invitrogen. The following antibodies were used for flow cytometry: FITC-Annexin V (556420), 7-AAD (559925) were from BD Biosciences; Alexa Flour® 488 anti-rabbit IgG was from Invitrogen. The following antibodies were used for immunoprecipitation and immunoblotting: anti-Bcl-3 (sc-185), anti-Caspase 8 (sc-6136), anti-STAT3 (sc-482), anti-UB (sc-8017), anti-rabbit IgG (sc-2027) and anti-mouse IgG (sc-2025) were from Santa Cruz; anti-Caspase 8 (9746), anti-cleaved Caspase 3 (9661), anti-pJNK (4668), anti-JNK (9252), anti-pIκB (2859), anti-PARP (9542), anti-FADD (2782), anti-A20 (5630), and anti-CYLD (8462) were from Cell Signaling Technology; anti-HA tag (51064) and anti-MYC tag (60003) were from Proteintech; anti-cIAP1/2 (MAB3400) was from R&D; anti-pSTAT3 (CY6566) was from Abways; anti-RIP1 (610458) was from BD Biosciences; anti-β-Actin (A2228), anti-Flag (F3165) and anti-Flag M2 affinity gel (A2220) were from Sigma Aldrich; anti-GAPDH (KC-5G4).
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10

Comprehensive Apoptosis Pathway Monitoring

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Monoclonal rabbit anti-NLRP3 (D2P5E, 13158 S), anti-caspase-9 (9502 T), anti-caspase-8 (1C12, 9746 S), anti-caspase-3 (9665 S), anti-cleaved-caspase-3 (Asp175, 9661S), anti-BID (2002S), anti-caspase-1 (2225S), anti-MLKL (14993S), Anti-pMLKL (S358, used in western blotting, 91689S), and anti-PARP-1 (9542S) were purchased from Cell Signaling Technology (Beverly, MA, USA). Polyclonal antibody anti-IL-1β (A1112) was acquired from Abclonal (Wuhan, China). Polyclonal rabbit anti-α-tubulin (11224-1-AP) was purchased from Proteintech (Chicago, IL, USA). Anti-pMLKL (S358, used in immunofluorescence assay and IHC, ab187091) was purchased from Abcam (Cambridge, UK). Anti-pMLKL (S345, used in IHC, MA5-32752) was purchased from Thermo Fisher (Waltham, MA, USA). Rabbit anti-RP3-NP antibody (RP3) and mouse-anti-SARS-CoV-2-NP (SR24) were made in-house.
LPS (L4391) was obtained from Sigma-Aldrich (St. Louis, MO, USA). VX-765 (S222), MCC950 (S7809), Z-VAD-FMK (S7023), Z-IETD-FMK (S7314), Z-DEVD-FMK (S7312), and NSA (S8251) were obtained from Selleck (Houston, TX, USA). MLN120B (HY-15473), GSK-872 (HY-101872), SM-164 (HY-15989), and staurosporine (HY-15141) were purchased from MedChemExpress (New Jersey, USA). TNF-α (300-01A) was obtained from Peprotech (Rocky Hill, NJ, USA). DAPI (4,6-diamidino-2-phenylindole, C1002) was purchased from Beyotime (Shanghai, China).
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