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12 protocols using tnf α

1

Western Blot Analysis of Inflammatory and Apoptotic Markers

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After the proteins were separated by electrophoreses, all samples were shifted to polyvinylidene difluoride membranes (Millipore Corporation, Massachusetts, USA). The membranes were incubated with the first Abs, NF-κB p65 (1:500), p-NF-κB p65 (1:500), TNF-α (1:500), Pro-IL-1β (1:1000), IL-6 (1:1000), IL-10 (1:500), Bad (1:750), Bcl-2 (1:500), Cyt C (1:1000), Cleaved-caspase 9 (1:500), Cleaved-caspase 3 (1:500), Cleaved-caspase 8 (1:1500), PI3K p110 (1:1000), AKT (1:500), p-AKT (1:500), MAP4 (1:500) (Wanlei Biotechnology Corporation, Shenyang, China), for 12~16 h at 4°C and then with the HRP conjugated anti-rabbit Ab (1:4000) (Wanlei Biotechnology Corporation, Shenyang, China) for 90 min at room temperature. Western blotting was monitored by using a chemiluminescence detection reagent (Meilun Biotechnology Corporation, Dalian, China) and visualized using Tanon 5200 Automatic Gel Imager (Tanon Science & Technology Corporation, Shanghai, China). For quantification, β-Tubulin (1:500) was used as the inner standards of tissue proteins.
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2

Western Blot Analysis of Metabolic and Inflammatory Proteins

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The protein samples were separated using 8%, 10%, and 12% sodium dodecyl sulfate–polyacrylamide gel electrophoresis and were transferred to polyvinylidene difluoride membranes (Cat# ISEQ. 00010, LOT# R6PA4145H; Merck Millipore, USA). The membranes were blocked with 5% skim milk for 3 h at 37°C and were incubated for 14 h at 4°C with the following diluted primary antibodies: pyruvate kinase (PK; 1:1,000; Wanlei, China), uncoupling protein 1 (UCP1; 1:1,500; Wanlei), succinate dehydrogenase (SDH; 1:500; Bioss), pyruvate dehydrogenase complex (PDHX; 1:500; Affinity, USA), lactate dehydrogenase (LDH; 1:1,000; Wanlei), poly ADP-ribose polymerase 1 (PARP1; 1:500; Proteintech, China), Cas8 (1:1,000; CST, USA), nuclear factor kappa B (NF-κB; 1:500; Wanlei), interleukin-1β (IL-1β; 1:1,000; Wanlei), and TNF-α (1:500; Wanlei). After washing thrice for 15 min each with phosphate-buffered saline with Tween 20, the membranes were incubated for 2 h at 37°C with peroxidase-conjugated secondary antibodies against rabbit IgG (Cat# sc-2357, RRID: AB_628497; Santa Cruz Biotechnology, Argentina). After washing three times by PBST for 15 min each again, the bound antibodies were visualized through chemiluminescence by using the ECL-plus reagent (GE Healthcare, UK). The GAPDH content was analyzed as the loading control by using a rabbit polyclonal antibody.
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3

Serum Biomarker Assessment in Rat Model

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All serum samples were tested for HMGB1 (FineTest, Wuhan, China), tumor necrosis factor-α (TNF-α) (Wanleibio, Shenyang, China), IL-1β (Wanleibio, Shenyang, China), and IL-6 (Wanleibio, Shenyang, China), using a rat ELISA kit. The ELISA assay was performed following the manufacturer's protocols. The optical density of each well was measured spectrophotometrically at 450 nm within 5 min after adding the stop solution using a microplate reader (ELX-800, BIOTEK, USA).
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4

Comprehensive Protein Expression Analysis

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Rabbit antibodies, such as TOM20 (WL0706), BAX (WL01637), BCL-2 (WL01556), cytochrome c (WL02410), caspase 3 (WL04004), iNOS (WL0992a), VDAC (WL02790), IL-2 (WL03259), TNF-α (WL01581), IL-1β (WLH3903), and β-actin (WL01372), were procured from Wanleibio in Shenyang, China, while rabbit anti-MFF (AF2365), anti-Mid49 (DF12044), anti-Mid51 (DF12019), anti-Opa1 (DF8587), and anti-Mfn1 (DF7543) were obtained from AFFINITY, Co., Ltd. This study acquired goat anti-rabbit IgG/HRP (PAB21463HRP-1000) secondary antibody (1 : 10000) from EarthOx (Millbrae, USA). The reagents and chemicals were all products of Sigma (St. Louis, USA). We procured SH-SY5Y cells from the Type Culture Collection of Chinese Academy of Sciences (Shanghai, People's Republic of China) and cultured them using DMEM/F-12 involving fetal bovine serum (FBS, 10%) and PS (penicillin–streptomycin, 1%). Meanwhile, BV2 microglial cells, which were purchased from the iCell Bioscience Inc., Shanghai, were cultured using DMEM (HyClone, UT, USA) involving FBS (10%; Gibco, CA, USA) and PS (1%). Male SD (Sprague–Dawley) rats, whose weights ranged from 250 to 280 g, were offered by Jinzhou Medical University. The present experimental protocol conformed to the National Guidelines for Animal Protection and gained approval from foregoing university's Institutional Animal Care and Use Committee.
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5

Serum Biomarker Quantification in Mice

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The enzyme‐linked immunosorbent assay (ELISA) kits were used to detect the expression level of IL‐6 (Wanleibio, China), IL‐1β (Wanleibio, Shenyang, China), TNF‐α (Wanleibio, Shenyang, China), Lactic dehydrogenase (LDH; Wanleibio, Shenyang, China), and total protein (TP; Nanjing Jiancheng Bioengineering Institute, China) in mice serum according to the manufacturer instructions.
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6

Molecular Mechanisms of LP-Mediated Cytoprotection

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LP was procured from Beijing Tongrentang Technology Development Co. (Beijing, China). D-Gal, >99% pure, was purchased from Sigma-Aldrich (St. Louis, MO, USA). The antibody to p-AMPK was purchased from Cell Signaling Technology (Boston, USA), and the antibody to SIRT1 was ordered from Affinity Biosciences (USA). The antibody to NF-κB (P65) was bought from BOSTER (Wuhan, China). The antibodies to AMPK, HO-1, IL-1, IL-6, and IL-10 were all purchased from Boiss (Beijing, China), and the antibodies to P21Waf1/Cip1, P16INK4A, and TNF-α were procured from Wanleibio (Shenyang, China). HRP-conjugated secondary antibodies were purchased from Boiss. The chemiluminescence reagents were from Affinity Biosciences (USA).
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7

Immunoblotting of Renal Proteins

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Renal tissue total protein and cellular total protein were extracted according to the previous method [35 ]. Nuclear proteins were extracted with a nuclear protein extraction kit. Immunoblotting was performed using antibodies from different companies: Nrf2 (1:1000), Keap-1 (1:1000), HO-1 (1:1000), and NQO1 (1:1000) (Beijing Biosynthesis Biotechnology Technology, Beijing, China); BAX (1:1000), Bcl-2 (1:1000), Caspase-3 (1:1000), Caspase-9 (1:1000) (ABclonal Co, Ltd., Wuhan, China); NF-kB (1:1000), TNF-α (1:1000) (Wanleibio, Harbin, China), and visualized using chemiluminescence agent ECL [36 ]. Image acquisition was performed using a celestial gel imaging system. Image analysis was performed using ImageJ software for densitometric analysis, and relative protein expression = target protein gray value/β-actin gray value. Details of antibodies are provided in Supplementary Table 1. The detailed methods were referred to the Supplementary 1.2.
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8

Investigating Liver Injury Pathways

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The liver tissues were lysed with Radio Immunoprecipitation Assay (RIPA) buffer (Beyotime, P0013B, Shanghai, China) or Nuclear Extraction Kits (Beyotime, P0028, Shanghai, China) supplemented with Protease Inhibitors (Beyotime, P1011, Shanghai, China). Then, Western blot was carried out as the general process. Primary antibodies: NF-κB (Cell Signaling Technology, 8242S, 1:1000, American), TNF-α (Wanleibio, WL01581, 1:1000), Nrf2 (Wanleibio, WL02135, 1:500, Shenyang, China), HO-1 (Wanleibio, WL02400, 1:500, Shenyang, China), Caspase-3 (Santa Cruz Biotechnology, sc-56053, 1:500, American), Bax (Cell Signaling Technology, 2772S, 1:1000, American), β-actin (Cell Signaling Technology, 4970S, 1:1000, American), and H3 (Proteintech, 17168-1-AP, 1:1000, American). Secondary antibodies: HRP-labeled goat anti-rabbit IgG(H + L) (Beyotime, A0208, Shanghai, China) and HRP-labeled goat anti-mouse IgG(H + L) (Beyotime, A0216, Shanghai, China).
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9

Protein Expression Profiling in Tissue Lysates

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RIPA buffer containing protease inhibitors (Beyotime) was used to lyse tissues. The primary antibodies were as follows: IL-6 (Wanleibio, Shenyang, China,), TNF-α (Wanleibio), Caspase-3 (Cell Signaling Technology, Danvers, MA, USA), iNOS (Santa Cruz Biotechnology, Santa Cruz, CA, USA), Bax (Cell Signaling Technology), SIRT 1 (Wanleibio), p53 (Wanleibio), p21 (Wanleibio), SA-β-gal (Cell Signaling Technology), p16 (Wanleibio), Nrf2 (Beyotime), HO-1 (Wanleibio), and β-actin (Wanleibio). The secondary antibodies were as follows: HRP-labeled goat anti-mouse and anti-rabbit IgG(H + L) (Beyotime).
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10

Cytokine Profiling in Rat Tissues

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Rat IL-1β, TNF-α (Multi Sciences Biotech, Lianke, China), MCP-1 (Enzyme-linked Biotechnology, China), and IL-6 enzyme-linked immunosorbent assay kits (Wanleibio, China) were used to evaluate the concentrations of IL-1β, TNF-α, MCP-1, and IL-6 in rat serum and/or lung tissue according to the manufacturers' instructions.
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