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19 protocols using timp1

1

Western Blot Analysis of Protein Targets

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Western blot analysis was carried out according to standard protocols. We used primary antibodies raised against GAPDH, CXCL13, ITLN1, HOXD9, and GPRC5B (Santa-Cruz Biotechnology, CA, USA), as well as TIMP1 and TSPAN11 (Proteintech, China). Goat anti-mouse and anti-rabbit antibodies conjugated with horseradish peroxidase were used as secondary antibodies (Jackson ImmunoResearch, PA, USA). We detected the blots by using enhanced chemiluminescence (Dura, Pierce, NJ, USA).
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2

Biochanin A Modulates Chondrocyte Inflammation

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Confluent rabbit chondrocytes were starved of serum overnight and pretreated with various concentrations of biochanin A for 2 h, followed by coincubation with IL-1β for 24 h. Cells were washed with ice-cold PBS and lysed with lysis buffer. The protein samples were separated by 12% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and transferred onto PVDF membranes. The membranes were blocked with 5% non-fat milk dissolved in TBST buffer and probed with primary antibodies against MMP-1, MMP-3, MMP-13, TIMP-1 (Proteintech, Chicago, IL), IκB-α, NF-κB p65, and β-actin (Cell Signaling Technology, Danvers, MA) at 4°C overnight. The membranes were washed with TBST and incubated with appropriate HRP-labeled secondary antibodies for 1 h at room temperature. Detection was carried out using enhanced chemiluminescent (ECL) substrate and exposure to Kodak X-Omat film (Kodak, Rochester, NY) according to the manufacturer’s protocols.
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3

Protein Expression Analysis Protocol

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Protein concentration was determined by the Bradford assay. 10% SDS-PAGE was used for protein separation. Protein bands were transferred onto a nitrocellulose (NC) membrane (PALL, USA), blocked with 5% (w/v) skim milk (BD, USA) in TBST (50 mM Tris, 100 mM NaCl and 0.1% Tween-20, pH 7.5) and incubated with primary antibodies FAM129A (1:1000, Proteintech, USA), GAPDH (1:2000, Proteintech, USA), TIMP1(1:1000, Proteintech, USA), MMP2 (1:500, Proteintech, USA), MMP9 (1:500, Proteintech, USA), MDM2 (1:500, Proteintech, USA), P53 (1:1000, Proteintech, USA), Bcl2 (1:1000, Wanleibio, China) and Bax (1:1500, Proteintech, USA) at 4 °C with shaking at 100 rpm overnight. The NC membrane was washed well with TBST for 3 × 10 min, incubated with HRP-conjugated Affinipure Goat Anti-Rabbit IgG (1:2000, Proteintech, USA) for 2 h at RT, and then washed again with TBST for 3 × 10 min. Protein bands were visualized by ECL and quantified by the Bio-Rad ChemiDoc™ MP system (Bio-Rad, USA).
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4

Liver Protein Biomarkers Analysis

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Total proteins were extracted from liver tissues and cells using radio-immunoprecipitation buffer (RIPA). Equal amounts of denatured proteins were separated on 10% SDS-PAGE and analyzed by immunoblotting with primary antibodies against GCLC (1:1000; Proteintech, 12601-1-AP), α-SMA (1:1000; Proteintech, 14395-1-AP), COL1 (1:1000; Abcam, ab6308), glucose-regulated protein 78 (GRP78; 1:1000; Proteintech, 11587-1-AP), CCAAT/enhancer-binding protein homologous protein (CHOP; 1:1000; Proteintech, 15204-1-AP), phosphorylated inositol-requiring enzyme 1 (p-IRE1; 1:1000; Abcam, ab48187), endoplasmic reticulum degradation enhancer, mannosidase alpha-like 1 (EDEM1; 1:500; Proteintech, 26226-1-AP); protein kinase inhibitor (p58IPK; 1:1000; Abcam, ab70840); nuclear factor kappa B (NF-κB; 1:1000; Proteintech, 14220-1-AP), inhibitor of KB kinase b (IKKB; 1:1000; Proteintech, 15649-1-AP), tumor necrosis factor α (TNFα; 1:1000; Abcam, ab6671), transforming growth factor 1 (TGFβ1; 1:1000; Proteintech, 21898-1-AP), tissue inhibitor of the metalloproteinase (TIMP1; 1:1000; Proteintech, 16644-1-AP), Matrix metalloproteinase 2 (MMP2; 1:1000; Proteintech, 10373-2-AP), and β-actin (1:10000; Proteintech, 14395-1-AP). After the incubation with HRP-conjugated secondary antibodies, the signals were visualized by the ECL system (Thermo Fisher Scientific).
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5

XLLXF Modulates Protein Expression in MDA-MB-231 Cells

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After the MDA-MB-231 cells were treated with XLLXF (50, 100, and 200 µg/mL) for 24 and 48 h, total cell protein lysates were extracted using RIPA lysis buffer that contained protease and phosphatase inhibitor cocktails. Protein lysates (20 µg), which were determined by BCA analysis (Beyotime, China), were loaded onto 10% SDS-PAGE gels. The protein bands were transferred onto NC membranes and blocked with 5% non-fat milk for 1 h at room temperature. The NC membranes with proteins were incubated with diluted primary antibodies at 4 °C overnight. The primary antibodies used in the analyses were as follows: VEGFA (1:1,000, Proteintech), MMP2 (1:1000, Proteintech), MMP9 (1:1000, Cell Signaling Technology), Vimentin (1:1000, Proteintech), VE-cadherin (1:1,000, Cell Signaling Technology), TIMP-1 (1:1000, Proteintech), TIMP-3 (1:1,000, Proteintech), and Twist1 (1:1000, Proteintech). The membranes were incubated with relative sources of secondary antibodies (1:5000) at room temperature for 1 h. Specific protein bands were recognized with Immobilon Western Chemiluminescent HRP Substrate (Millipore, MA, USA). Image J software was used for image analysis.
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6

Protein Expression Analysis in Lung Tissues

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Total protein was extracted from lung tissues or cells using Tissue or Cell Total Protein Extraction Kit (Sangon Biotech). Equivalent protein from different samples was separated by protein electrophoresis, following by transformation onto PVDF membranes (Merck Millipore, Billerica, MA, USA). The membranes were incubated with the anti-rabbit SIRT1, TIMP-1, MMP-9, CHOP, GRP78, caspase-12 or caspase-3 antibodies (1:1000 dilution, Proteintech, Wuhan, China) at 4 °C overnight after immersed into blocking buffer. After the membranes were washed with TBST for several times, goat anti-mouse IgG antibody (1:5000, Proteintech) labelled with horseradish peroxidase were incubated with the membranes as a secondary antibody. Anti-mouse β-actin antibody (1:5000, Proteintech) was used as a reference protein for normalization. The grey levels of the protein bands were examined by Image J software.
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7

Liver Fibrosis Mechanistic Pathways

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Propylene glycol alginate sodium sulphate was purchased from Dalian Tianyu Pharmaceuticals Co., Ltd and disposed in saline to obtain different drug doses of 12.5, 25 and 50 mg/kg, and stored at 4°C.12 CCl4 was acquired from Sinopharm. Microplate test kits of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were obtained from Nanjing Jiancheng Bioengineering Institute (Jiancheng Biotech). Antibodies against IL‐6, Col‐1, α‐SMA, TGF‐β1, MMP‐2, TIMP‐1, Beclin‐1, p62, Smad2 and Smad3 were purchased from Proteintech, and those against p‐Smad2, p‐Smad3, JAK2, STAT3 and p‐STAT3 were purchased from Cell Signaling Technologies. The polymerase chain reaction (PCR) kit was acquired from Takara Biotechnology.
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8

Comprehensive Protein Analysis of Cell Lysates

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Cells or tissues homogenate were lysed by Ripa lysis buffer (KeyGEN Bio TECH) containing protease and phosphatase inhibitors. The extracted proteins were quantified using BCA Protein Assay Kit (Thermo Scientific) and WB analysis of MMP1 (1:1000, Proteintech), MMP9 (1:1000, Proteintech), TIMP1 (1:1000, Proteintech), COL1A1 (1:1000, CST), COL3A1 (1:1000, Santa), NLRP3 (1:1000, NOVUS), N-GSDMD (1:1000, Affinity), Caspase1 (1:1000, CST), IL-1β (1:1000, Affinity), iNOS (1:1000, Proteintech), Arg-1 (1:1000, CST), SOD (1:1000, Proteintech) and GSH were conducted following the standard methods provided by Cell Signaling Technology and quantified using Image J software.
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9

Evaluating FAM129A, MMP9, and TIMP-1 in HCC

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Expression levels of FAM129A (Proteintech, USA), MMP9 (Proteintech, USA) and TIMP-1 (Proteintech, USA) were determined by IHC assay in HCC tissue arrays. A biotin-streptavidin horseradish peroxidase (HRP) detection system (ZSGB-BIO, China) was used to treat samples according to the manufacturer’s guidelines and a DAB (diaminobenzidine) kit (ZSGB-BIO, China) was used to envision images using a BX63 microscope (Olympus, Japan). Score I represents IHC immunoreactive intensity and was classified into four ranks, 0 (negative), 1 (weak), 2 (moderate) and 3 (strong), whereas Score II signifies the observed positively stained cells, and the DAB staining level of each sample was categorized as 0 (none), 1 (1–10% cells per field), 2 (10–50%), 3 (51–75%) and 4 (>76%). The IHC immunoreactivity degree is the product of Score I and Score II and ranges from 0 to 12. The scores were considered in following way: 0–2 as negative (−), 3–5 as weak (+), 6–8 as moderate (++), and 9–12 as strong (+++). Scoring of IHC assays was done independently by two experienced pathologists.
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10

Western Blot Analysis of Bone Markers

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Cells at the logarithmic phase were harvested and lysed with radioimmunoprecipitation assay (RIPA) buffer [150 mM NaCl, 1% NP-40, 0.25% Na-deoxycholate, 1 mM ethylenediaminetetraacetic acid (EDTA), 50 mM Tris-HCl, pH 7.4]. Total protein and nuclear proteins were extracted. Proteins were separated by 10% sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) and transferred onto polyvinylidene difluoride (PVDF) membranes (Millipore, Billerica, MA, USA). The membranes were incubated with a primary antibody overnight at 4 °C, followed by a secondary antibody (Zhongshan Bio-Tech Co, Beijing, China) for 1 h at room temperature. Then, the membranes were scanned using an Odyssey infrared imaging system (LICOR, Lincoln, NE, USA). The primary antibodies against Mmp13, Timp1, Bsp, Runx2 (Proteintech Group, Inc., Wuhan, China), and GADPH (KangChen Biotech, Shanghai, China) were used for western blot analysis.
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