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30 protocols using ab228402

1

Antibody-based Exploration of Inflammatory Pathways

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Antibodies against MMP-9 (ab228402), V5 (ab27671), Integrin β3 (ab119992), ICAM-1 (ab222736), VCAM-1 (ab134047), TRAF-6 (ab33915) and β-actin (ab8227) were purchased from Abcam. Anti- Integrin β5 (#3629), and NF-κB proteins (NF-κB Pathway Sampler Kit #9936) were purchased from Cell Signaling Technology. Pierce™ Protein A/G Plus Agarose was obtained from Invitrogen. LPS, rhodamine B isothiocyanate-dextran, and p-aminophenylmercuric acetate (APMA) were purchased from Sigma-Aldrich. Murine recombinant MMP-9 (R&D, 909-MM), MMP-9 ELISA kits (MMPT90), IL-6 ELISA kits (M6000B), TNF-α ELISA kits (DY410), CXCL-1 ELISA kits (MKC00B), and MPO ELISA kits (DY3667) were from R&D Systems. MMP-9 neutralizing monoclonal antibody (IM09L) was from Sigma-Aldrich. NF-κB inhibitor, PDTC, and ROS scavenger, N-acetyl-L-cysteine (Nac), were obtained from MedChem Express (Shanghai, China). LipoJet™ reagent and GeneMute siRNA transfection reagent were purchased from SignaGen (Ijamsville, MD, USA).
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2

Targeting Circular RNA in Xenograft Tumor Model

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Three groups of five nude mice (BALB/c/nu/nu, male, Beijing Vital River Laboratory Animal Technology, Beijing, China) each were subcutaneously injected with A498 cells or A498 cells stably transfected with sh-circ_0054537 vector or sh-con. In brief, 2 × 106 cells in 100 μL normal saline were used to cell inoculation, and equal volume of normal saline was used in Mock group. The xenograft tumors were examined every week for 4 weeks, and the larger and shorter sizes (l and s) in perpendicular indexes were measured by vernier caliper. The weight of tumors were examined on electronic scales on the last day after the mice were euthanized. The tumor volume was calculated as 0.5 × l× s2. The tumor tissues were restored for further total RNA/protein isolation or immunohistochemistry of paraffin embedding (IHC-P) [27 (link)]. Antibodies were MMP-9 (ab228402; 1:5,000; Abcam), Bax (ab216494; 1:500; Abcam) and ki-67 (ab15580; 1:50; Abcam). Animal experiments were approved by the Ethics Committee of The Fourth Hospital of Hebei Medical University. All the animals were subjected to humanitarian care, and all experiments were performed in accordance with the Guide for the Care and Use of Laboratory Animals (Ministry of Science and Technology of China, 2006).
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3

Investigating Inflammatory Mediators in Lung Injury

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The primary antibodies used for western blotting included: MMP9 (ab228402, Abcam, USA), β-actin (RM2001, Beijing Ray, Beijing, China).
The primary antibodies used for IHC included: S100A9 (ab242945, Abcam), Ly6G (ab238132, Abcam), CD11b (ab133357, Abcam), F4/80 (70,076 S, CST, Danvers, MA, USA), IL-1β (12,242 S, CST), MMP9 (ab228402, abcam).
The primary antibodies used for immunofluorescence (IF) included: CD11b (ab133357, Abcam), F4/80 (70,076 S, CST), IL-1β (12,242 S, CST), MMP9 (ab228402, abcam), SPC (ab211326, abcam).
The primary antibodies used for flow cytometry included: TruStain FcX anti-mouse CD16/CD32 antibody (Biolegend, 101,319), FITC anti-mouse/human CD11b (Biolgend, 101,205), PE/Cyanine7 anti-mouse Ly-6G (Biolegend, 127,617), Alexa Fluor 647 Rat anti-mouse S100A9 (BD Pharmingen, 565,833) and PE anti-mouse IL-1β (Thermo, 12-7114-80).
Other reagents included: Cultrex Basement Membrane Extract (R&D, Minneapolis, MN, USA); recombinant murine IL-1β (Peprotech, Rocky Hill, USA), murine SAA3 (General Biol, China); IKK 16, JNK-IN-7, Losmapimod and Ravoxertinib (MedChemExpress, Monmouth Junction, NJ, USA).
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4

Anti-inflammatory Mechanisms of Chlorogenic Acid in BV-2 Cells

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BV-2 cells were purchased from the Cell Bank of the Chinese Academy of Sciences. Lipopolysaccharide (LPS) was purchased from Sigma−Aldrich (St. Louis, MO, USA). Chlorogenic acid was purchased from Shanghai Yuanye Biotechnology Co. Ltd. (Shanghai, China). Anti-iNOS (1:1000, ab178945) and anti-MMP9 (1:1000, ab228402) were purchased from Abcam. Anti-CD86 (1:1000, BM4121), anti-Arg-1 (1:1000, M01106-4), anti-IL-10 (1:1000, RP1015), anti-CD206 (1:1000, A02285-2), anti-CXCL12 (1:1000, BA1389), anti-CXCR4 (1:1000, A00031-4), anti-PTGS2 (1:1000, A00084), and anti-TNF (1:1000, BA0131) were purchased from Boster Biological Technology Co. Ltd. (Shanghai, China). Cleaved caspase-3 (1:500, GB11532), IBA-1 (1:500, GB12105), and CD206 (1:400, GB113497) were purchased from Wuhan Servicebio Biotechnology Co. Ltd. (Wuhan, China). p-Akt1 (1:1000, 9018S), Akt1 (1:1000, 75692S), p-NF-κB (1:1000, 3033S), NF-κB (1:1000, 8242S), p-ERK1/2 (1:1000, 4370T), ERK1/2 (1:1000, 4696S), p-P38 (1:1000, 4511T), and P38 (1:1000, 8690T) antibodies were purchased from CST.
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5

Comprehensive Protein Detection Protocol

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Primary antibodies include anti-Bach2 (Abcam, ab83364, ab243148; Santa Cruz, sc-14704), anti-Bach1 (Santa Cruz, sc-14700), anti-Nrf2 (Abcam, ab62352), anti-HO-1 (Enzo, ADI-SPA-896-D), anti-p21 (Abcam, ab109520), anti-p16 (Santa Cruz, sc-166760), anti-Lamin B1 (Santa Cruz, sc-6217), anti-Lamin A/C (Santa Cruz, sc-6215), anti-Atg3 (CST, 3415), anti-Atg5 (CST, 12994), anti-Atg7 (CST, 8558), anti-Beclin-1 (CST, 3495), anti-LC3A/B (CST, 12741), and anti-p62 (CST, 88588), anti-MMP3 (Abcam, ab52915), anti-MMP9 (Abcam, ab228402), anti-IL-6 (Abcam, ab229381), anti-CXCR2 (Abcam, ab65968), anti-Ub (Abcam, ab134953).
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6

Protein Extraction and Western Blot Analysis

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Proteins were extracted from the cerebral cortex or cultured cells using the Membrane and Cytosol Protein Extraction Kit (Beyotime, China) and measured with the BCA Protein Assay Kit (Beyotime, China). Fifty micrograms protein per sample was separated through 10% ExpressPlus™ Gels (GenScript, the USA) and then transferred to Polyvinylidene fluoride (PVDF) membranes. After blocking with 5% skim milk in buffer, the membranes were incubated overnight at 4°C with the following antibodies: Caspase‐1 (89332, CST), Cleaved Caspase‐3 (ab214430, Abcam), COX‐2 (12282, CST), p‐JNK (ab124956, Abcam), JNK (ab179461, Abcam), p‐P38 (4511, CST), P38 (8690, CST), BAX (ab32504, Abcam), Bcl‐2 (ab182858, Abcam), MMP‐2 (87809S, CST), MMP‐9 (ab228402, Abcam), Catalase (ab76110, Abcam), Cu/Zn SOD (ab13498, Abcam), β‐actin (4970, CST), CD63 (EXOAB‐CD63A‐1, SBI), CD81 (EXOAB‐CD81A‐1, SBI), CD9 (EXOAB‐CD9A‐1, SBI), Rac1 (8631, CST), Cdc42 (8747, CST), PAK‐1(ab223849, Abcam) and p‐PAK1 (ab75599, Abcam). The membranes were washed and incubated with the secondary antibodies for 2 hours, and the positive bands were detected with a chromogenic developing agent.
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7

Immunohistochemical Analysis of Tissue Markers

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Immunohistochemical analysis was performed as described previously (Pakharukova et al., 2019b (link); Kovner et al., 2019 (link)). Antibodies and dilutions used in this study were as follows: anti–alpha-smooth muscle actin (α-SMA; 1:200; cat. # ab7817, Abcam), anti-MMP9 (1:200; cat. # ab228402, Abcam), anti-collagen 1 alpha (1:200; cat. # ab34710; # ab53444, Abcam), anti-E-cadherin (1:200; cat. # ab76055, Abcam), and anti–N-cadherin (1:200; # ab76011, Abcam) antibodies with the respective secondary antibodies: a cyanine 3–conjugated goat anti-mouse IgG (H + L) cross-adsorbed antibody (1:500; cat. # M30010, Invitrogen, USA) or a GFP-conjugated AffiniPure goat anti-rabbit IgG (H + L) antibody (1:1000; cat. # 111–095-003, Jackson AB, USA) and a mouse anti-rabbit IgG-CFL 555 antibody (sc-516,249, Santa Cruz, USA). The slices were coverslipped with the Fluoro-shield mounting medium containing 4′,6-diamidino-2-phenylindole (DAPI; cat. # F6057, Sigma-Aldrich, USA) and examined under an Axioplan 2 microscope (Zeiss, Germany).
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8

Protein Expression Analysis in SKOV3 and HO8910

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The total proteins were extracted from SKOV3 and HO8910 cells and quantified by BCA protein analysis kit (Beyotime), then separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). After separation, each protein was transferred to a polyvinylidene fluoride (PVDF) membrane (Millipore, USA), which was blocked with 5% skimmed milk at room temperature for 2 h and then incubated with the corresponding primary antibody overnight at 4 ℃. The membrane was washed three times with phosphate buffer solution with 0.1% Tween-20 (PBST) for 10 min each time, and incubated with secondary antibody at 37 ℃ for 1 h. Protein bands were visualized using an imaging system and enhanced chemiluminescence (ECL) reagents (Millipore, USA). β-actin was used as an internal control, and the results were analyzed using ImageJ software. The primary antibodies used were: β-actin (1:500, ab115777, Abcam), Ki67 (1:1,000, ab16667, Abcam), matrix metalloproteinase (MMP)9 (1:1,000, ab228402, Abcam), MMP2 (1:1,000, ab92536, Abcam), and ESR1 (1:1,000, ab108398, Abcam).
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9

Quantitative Proteomics of Ectopic Lesions

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The total proteins of ectopic lesions in EMS mice were extracted using radio-immunoprecipitation assay (RIPA) buffer (Beyotime, China) supplemented with protease and phosphatase inhibitors (Sigma, USA). The protein concentration was measured using a BCA protein assay kit (Beyotime, China). After denaturation, equal amounts of proteins were separated via SDS-polyacrylamide gel electrophoresis (PAGE) before wet transfer onto polyvinylidene difluoride membranes. Nonspecific binding sites were blocked by incubating the membranes with 5% skim milk in Tris-buffered saline with 0.1% Tween 20 (TBS-T) for 1 h. Then, the membranes were incubated overnight at 4 °C with primary antibodies (1:1000) against MMP9 (#ab228402, Abcam, UK), MMP2 (#87809, CST, USA), BCL2 (#2870, CST, USA) and GAPDH (#10112, Arigo, China). Subsequently, membranes were incubated with appropriate horseradish peroxidase-conjugated anti-rabbit (#65351, Arigo, China) or anti-mouse (#65350, Arigo, China) IgG secondary antibodies for 1h at room temperature. After three washes with TBS-T, immunopositive bands on the blots were visualized using chemiluminescent HRP substrate (#WBKLS0100, Millipore, USA) on the enhanced chemiluminescence detection system (Merck Millipore, USA).
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10

Western Blot Analysis of Inflammation Markers

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Cells were lysed in cell lysis buffer (Thermo Fisher Scientific, Pittsburgh, USA). The protein concentration in the cell homogenate was determined using a bicinchoninic acid (BCA) assay kit (Beyotime, Shanghai, China). SDS-PAGE separated the proteins (30 μg), which were subsequently transferred onto polyvinylidene fluoride (PVDF) membranes (Biorbyt, Cambridge, UK). After blocking with 5 % skim milk for 2 h, the membranes were incubated overnight at 4 °C with rabbit antibodies against GBP5 (1:2000, 13,220–1-AP, Proteintech, Wuhan, Hebei, China), IRF1 (1:1000, 8478s, CST, Boston, USA), MMP9 (1:1000, ab228402, Abcam, MA, USA), MMP13 (1:1000, bs10581 R, Bioss, Boston, MA, USA), COL2A1 (1:1000, ab34712, Abcam), aggrecan (1:1000, AF6126, Beyotime), Sox9 (1:1000, BS1597, Bioworld, Nanjing, Jiangsu, China), NLRP3 (1:1000, bs1001 R, Bioss), Caspase1 (1:1000, BS5641, Bioworld), GSDMD (1:1000, ab219800, Abcam), Pro-IL-1β (1:1000, ab216995, Abcam), Pro-Caspase1 (1:1000, ab179515, Abcam), and GAPDH (1:1000, 5174s, CST, Boston, USA). Subsequently, the membranes were incubated with secondary antibodies (1:20,000, BS13278, Bioworld) at room temperature for 1.5 h. After washing the membranes in TBST, chemiluminescent signals were detected using a Bio-Rad Molecular Imager ChemiDocTM XRS + system (Bio-Rad, Hercules, CA, USA), with GAPDH serving as the loading control.
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