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95 protocols using cox 2

1

Immunostaining of Tissue Sections

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OCT-embedded frozen (8 µm), or formalin-fixed and paraffin-embedded (5 µm) tissue sections were used for histology and immunostaining. Immunofluorescence staining and immunohistochemistry were carried out with antibodies described below. For formalin-fixed tissues, antigen retrieval was performed with citrate buffer at 92 °C for 30 min. Antibodies against Ki-67 (#14-5698, 1:300) were obtained from eBioscience, ph-H3 (#3377, 1:400) from Cell Signaling, Cox-2 (#160106, 1:200) from Cayman Chemical, Krt7 (#ab181598, 1:600) from Abcam, and Krt5 (#PRB-160P and # SIG-3475, 1:600), Krt6 (#PRB-169P, 1:600), Krt15 (#PCK-153P, 1:400), CD324 (#147306, 1:300), CD45 (#103101, 1:400), Gr-1 (#108417, 1:400), Ly-6G (#127625, 1:400), F4/80 (#123101, 1:600), and CD3 (#100201, 1:400) from BioLegend.
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2

Western Blot and Zymography Analysis

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Cell or tissue extracts (in RIPA buffer, containing 1% Triton X-100, 1% sodium deoxycholate, 0.1% SDS, 150 mM NaCl, 10 mM Tris HCl, pH 7.4, 1 mM EDTA, protease inhibitors [Roche], and phosphatase inhibitors [Sigma-Aldrich]) were subjected to 10% SDS-PAGE and subsequently transferred to a nitrocellulose membrane (Whatman GmbH). Membranes were probed with antibodies against p-STAT3 (Call Signaling Technology), COX2 (Cayman), STAT3, IκBα, and β-actin (Santa Cruz Biotechnology, Inc.). For detection of MMP9 in cell culture or whole-colon culture supernatants, these were analyzed on 8% SDS-PAGE containing 1 mg/ml gelatin under nonreduced conditions at 4°C. Gels were washed in 2.5% Triton X-100 for 1 h, incubated in MMP activation buffer (50 mM Tris-HCl [pH 7.5], 5 mM CaCl2, 0,02% NaN3, and 1 µM ZnCl2) for 18 h at 37°C and stained with 0.5% Coomassie blue R250. Quantification of bands from Western blot or zymography was performed with ImageJ software (National Institutes of Health).
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3

Caffeic Acid Regulates COX-2 Expression

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After the collection of the culture medium for the analysis of PGE2 (see above), we added ice-cold Radioimmunoprecipitation assay (RIPA) buffer with protease inhibitors to the cells and extracted the cellular protein as described elsewhere [19 (link)]. The protein analyzed by Western blot was quantified (DC colorimetric assay, Bio-Rad, Warsaw, Poland), loaded in SDS-PAGE at 10% (20 µg of protein in each lane), and separated. Next, it was transferred to PVDF membranes, which were blocked (5% albumin, w/v), and then incubated with primary (COX-2, 1:1000 and Glyceraldehyde 3-phosphate dehydrogenase -GAPDH-, 1:2500; Cayman, San Diego, CA, USA) and secondary (goat anti-mouse and anti-rabbit, 1:10,000; LI-COR antibody, Lincoln, NE, USA) antibodies using the same conditions previously described elsewhere [19 (link)]. Odyssey Infrared Image System v. 1.2 (Li-COR Bioscience, Lincoln, NE, USA) allowed the detection and quantification of the proteins. The effect of caffeic acid on COX-2 expression was determined from three different replicates (n = 3).
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4

Profiling SIRT Family Expression in Gingival Tissues

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Total RNA was isolated from human gingival tissues and primary culture human GF using TRIzol reagent (Ambion, Carlsbad, CA, USA). Non-inflamed or inflamed human gingival tissues were homogenized in TRIzol reagent using a glass tissue grinder. RNA was reverse-transcribed, and the complementary DNA was amplified by PCR using Taq polymerase (GeneAll, Songpa, Seoul, Republic of Korea). Quantitative real-time PCR (qRT-PCR) was performed using an iCycler (Bio-Rad Laboratories, Hercules, CA, USA) and the SYBR premix Ex Taq (Takara Bio, Kyoto, Japan). All qRT-PCR was performed in duplicate, and the target gene amplification signal was normalized to that of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in the same reaction. The relative levels of SIRT family (SIRT1–7) gene expression were analyzed using the comparative Ct (cycle threshold) method. The average Ct was calculated for SIRT1 to SIRT7 and GAPDH, as previously described.26 (link) Primers and experimental conditions are shown in Supplementary Table 1. Western blot analysis was performed to detect the cellular and secreted levels of NAMPT, COX-2 and MMP3 in total cell lysates or in conditioned culture media using standard techniques. The following primary antibodies were used for western blotting: NAMPT (AdipoGen), MMP3 (Abcam), COX-2 (Cayman) and TUBULIN (Sigma-Aldrich).
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5

COX-2 Expression in RAW264.7 Cells

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To study COX-2 protein expression, RAW264.7 cells were treated for 6 hours with LPS or BLP (25 ng to 100 ng/ml). Lysates were prepared using Radio-Immunoprecipitation Assay (RIPA) buffer and immunoblots were developed using specific primary and appropriate secondary antibodies for COX-2 (Cayman Chemicals, MI, USA) and GAPDH (Fitz Gerald Industries, MA, USA). The bands were visualized using SuperSignal West Pico ECL assay kits.
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6

Quantifying COX-2 Enzyme Levels

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A 5000 unit, 11.9 μM stock solution of COX-2 was obtained from Cayman Chemical. All buffers were prepared using high-purity water (Cayman Chemical). Protein concentrations were used based on the units described by the vendor and validated by SDS-PAGE analyses.
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7

Western Blot Analysis of Protein Targets

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Western blots were performed as described [12 (link)] using antibodies against HuR (clone 3A2, Santa Cruz Biotechnology) at a dilution of 1:20,000 for 1 hr at RT and COX-2 (160126, Cayman Chemical) at a dilution of 1:1000 for 16 hours at 4°C. Caspase 3 cleavage was detected using rabbit polyclonal anti-Caspase 3 (9662, Cell Signaling) at a dilution of 1:1000 for 16 hr at 4°C. Membranes were stripped and re-probed using β-actin antibody (Clone C4; MP Biomedicals). Cytoplasmic lysates were obtained using NE-PER cytoplasmic extraction reagent (Thermo Scientific) using α-tubulin (322500, 1:20,000 dilution, Invitrogen) and Lamin A/C (2032S, 1:2,000 dilution, Cell Signaling) as cytoplasmic and nuclear loading controls, respectively. Detection and quantitation of blots were carried out as described [10 (link)].
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8

Western Blotting for Protein Analysis

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Western blotting was carried out as previously described16 (link). Antibodies used in this study were listed as follows: CFTR (1:200, Cat#ACL-006, Alomone labs, Jerusalem, Israel), COX-2 (1:200, Cat#160106, Cayman chemical, Ann Arbor, USA), P-JNK (1:1000, Cat#9255, Cell Signaling Technology, Boston, USA), JNK (1:1000, Cat#9252, Cell Signaling Technology), P-Erk1/2 (1:1000, Cat#4370, Cell Signaling Technology), Erk1/2 (1:1000, Cat#4695, Cell Signaling Technology), P-IκBα (1:500, Cat#AB55066, Sangon Biotech), GAPDH (1:5000, Cat#KC-5G5, Kangcheng Biotech, Shanghai, China), Tubulin (1:500, Cat#10759-1-AP, Proteintech, Chicago, USA) and β-actin (1:1000, Cat#60008-1-lg, Proteintech).
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9

COX-2 Protein Expression Analysis in Huh-7 Cells

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Huh-7 cells were seeded in 24-well plates at a density of 5 × 104 cells per well overnight and treated with indicated reagent at proper concentrations for three days. Cells were washed with cold phosphate-buffered saline (PBS) and lysed by radioimmunoprecipitation assay (RIPA) lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1% Nonidet P-40, 2 mM ethylenediaminetetraacetic acid (EDTA), 1 mM ethylene glycol bis(2-aminoethyl)tetraacetic acid (EGTA), 1 mM NaVO3, 10 mM NaF, 1 mM dithiothreitol (DTT), 1 mM phenylmethylsulfonyl fluoride (PMSF), 25 μg/mL aprotinin, and 25 μg/mL leupeptin) and stored at −20 °C. The protein concentration was determined by the Bradford method. Then, 10-μg protein samples were separated by 10% SDS-PAGE and transferred onto a polyvinylidene fluoride (PVDF) membrane. The membrane was blocked with 5% non-fat dried milk and incubated with specific antibodies against GAPDH (1:10000, Genetex, Irvine, CA, USA) and COX-2 (1:1000; Cayman Chemical, Ann Arbor, ML, USA). Antibodies were diluted in 5% milk containing Tris-buffered saline (TBS) and 0.5% Tween. The blotting signal was developed using an enhanced chemiluminescence (ECL) detection kit (PerkinElmer, Waltham, MA, USA) and was counted by the software Quantity One (Bio-Rad, Hercules, CA, USA).
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10

Antibody Reagents for Inflammation

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CGA was purchased from Sigma-Aldrich (St. Louis, MO, USA). The following antibodies were used in this study: inducible nitric oxide synthase (iNOS; Transduction Laboratories, San Jose, CA, USA), cyclooxygenase-2 (COX-2; Cayman, Ann Arbor, MI, USA) and β-actin antibody (Sigma-Aldrich).
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