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11 protocols using sodium dodecyl sulfate polyacrylamide gel electrophoresis sds page

1

Investigating Autophagy Regulation in Cells

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CCK-8 (Cell Counting Kit-8) reagent was purchased from Dojindo (Tokyo, Japan). The autophagy protein 5 (ATG5), microtubule-associated protein light chain 3 (LC3), p-p65, p65, and IκBα primary antibodies for Western blotting were purchased from Cell Signaling Technology (Massachusetts, USA), and the other reagents used for Western blotting, including the horseradish peroxidase-conjugated secondary antibodies, radioimmunoprecipitation assay (RIPA), polyvinylidene difluoride (PVDF) membranes, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) were obtained from Beyotime (Shanghai, China). The p65 primary antibody for immunofluorescence was supplied by Abcam (Cambridge, UK). Adenovirus expressing green fluorescent protein–microtubule-associated protein light chain 3(GFP–LC3) was purchased from Genomeditech (Shanghai, China). Acridine orange (AO), TNF-α, DHA, and SM7368 were purchased from Sigma-Aldrich (St. Louis, MO, USA).TRIzol and the SYBR Premix Ex Taq mixture were obtained from Takara (Takara Bio, Otsu, Japan).
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2

Quantifying Placental Angiogenic Factors

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Placental VEGF (ab32152, Abcam), eNOS (ab76198, Abcam), and CRP (ab211631, Abcam) levels were detected using Western blotting. RIPA (Beyotime) was used to extract the proteins from the tissues. The sample concentration was then determined using the BCA method. Loading buffer (Beyotime) was added to the samples and they were incubated at 99°C for 10 minutes. These samples were separated using 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE; Beyotime). Then these proteins were transferred to a polyvinylidene fluoride (PVDF) membrane (Millipore, Billerica, MA, USA), and the membrane was blocked with 5% skimmed milk powder and incubated with the primary antibody at 4°C overnight. The next day, the membrane was washed with the phosphate buffered saline Tween-20 (PBST) three times. The membrane was then incubated with the second antibody at the room temperature for 2 hours, and the membrane was washed with the PBST three times and exposed using a Tanon 4600 (Tanon Co., Shanghai, China).
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3

Western Blot Analysis of Fgf9 Expression

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Tissue collected from the anus and rectum of the ARM model and normal rat embryos was pooled and sonicated in double-distilled H2O containing protease inhibitors. Protein extracts (50 μg) were denatured by heating at 90°C for 5 min and then stored at −80°C refrigerator until used. Protein samples were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE; Beyotime, Shanghai, China), transferred to the polyvinylidene fluoride (PVDF) membranes (Millipore, Billerica, MA, USA), blocked with 5% fat-free milk in Tris-buffered saline for 1.5 h at room temperature, and incubated overnight at 4°C with primary anti-Fgf9 rabbit polyclonal antibody (Abcam, Cambridge, UK; 1 : 1000 dil). The membranes were incubated with horseradish peroxidase-conjugated goat anti-rabbit secondary antibody (Beyotime, Shanghai, China; 1 : 1000 dil) for 2 h at room temperature. A chemiluminescent substrate kit (BeyoECL Star; Beyotime, Shanghai, China) was used to detect the immunostained bands. In each lane, β-actin was used as an internal standard to normalize protein expression.
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4

Western Blot Analysis of Apoptosis Markers

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Protein expressions of GPX1, PTEN, PDK-1, AKT, Bcl-2, Bax, and Nf-κB were detected by western blot using specific primary antibodies (Gene Tex, Irvine, California, US). Antibody against GAPDH (Kangcheng Biology, Shanghai, China) was used as a loading normalization control. After BAY 11-7082 treatment or transfection experiments, the cells were collected and the total protein was extracted from the cells. Protein (30 μg) was loaded and separated using a 10% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) (Beyotime, Shanghai, China) gel and transferred to an Immobilon-P Transfer Membrane (PVDF) (Beyotime, Shanghai, China). The membranes were blocked with 5% nonfat milk in Tris-buffered saline (TBS) containing 0.1% Tween-20 for 1 h at room temperature. The blots were probed with the selected primary antibodies overnight at 4°C, washed in TBST, and further incubated with a species-specific horseradish peroxidase-conjugated secondary antibody (anti-rabbit, ExCell Bio, Shanghai, China) for 1 hour at room temperature. The western blot process was performed according to standard protocols. An enhanced chemiluminescence detection method (Pierce ECL Western Blotting Substrate) (Thermo Scientific, Belmont, Massachusetts, US) was used to visualize the blots.
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5

Western Blot Analysis of Inflammatory Mediators

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Cells were lysed in radio immunoprecipitation assay (RIPA) lysis buffer (Beyotime Institute of Biotechnology, Shanghai, China) containing proteinase and phosphatase inhibitors. A BCA assay kit (Beyotime) was used to measure the concentration of protein. The supernatant proteins were precipitated. The protein of lytic samples was transferred to polyvinylidene fluoride (PVDF) membranes (Beyotime, China) after separating by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) (Beyotime). Membranes were incubated with antibodies against gasdermin D (GSDMD, Abcam, Cambridge, UK), IL-1β (Abcam), nuclear factor of activated T-cells, cytoplasmic 1 (NFATc-1, Abcam), TRAP (Abcam), pro caspase-1 (Cell Signaling Technology, Danvers, MA, USA), cleaved caspase-1 (Cell Signaling Technology), ASC (Cell Signaling Technology), TNF receptor-associated factor (TRAF) 2 (Proteintech, Rosemont, IL, USA), TRAF6 (Proteintech), c-Fos (Proteintech), cathepsin K (CTSK, Proteintech), matrix metalloprotein 9 (MMP9, Proteintech), and anti-actin (Beyotime) overnight at 4 °C after blocking with quick block buffer (Beyotime) for 30 min. Then, membranes were washed three times with TBS-Tween and incubated with the appropriate secondary antibody for 1 h at room temperature. The results were visualised via chemiluminescent peroxidase substrate (Proteintech).
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6

Dextran Sodium Sulfate-Induced Colitis Model

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Dextran sodium sulfate (DSS; molecular weight, 36,000 to 50,000) was purchased from MP Biomedicals (Solon, OH, USA). Freeze-dried bacteria powder containing 1.6×1011 colony-forming units (CFU)/g of B. infantis was provided by Shandong Sinovac Biotech Co., Ltd. (Number: 2017012; Beijing, China). We purchased antibodies specific for the following proteins for immunohistochemical and Western blot experiments: PD-L1, PD-1, Foxp3 (Proteintech Group, Inc., Chicago, IL, USA), IL-10, TGF-β1, and GAPDH (Abcam, Cambridge, UK). The remaining reagents were obtained from the indicated sources. The Polymer Horseradish Peroxidase Detection System for rabbit primary antibody, the diaminobenzidine (DAB) kit, and Peroxidase-Conjugated AffiniPure goat anti-rat IgG were from ZSGB-BIO Co. (Beijing, China), and the enhanced BCA protein assay kit and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) reagents were from Beyotime Institute of Biotechnology (Jiangsu, China).
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7

Western Blot Analysis of Apoptosis Regulators

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The total proteins in each group were extracted with a protein extraction kit (Camilo Biological, Nanjing, China). The protein concentration was quantified by bicinchoninic acid (BCA) method (Pierce, Rockford, IL, USA), and the protein was denatured by boiling for 10 min. 20 μg of the protein sample was electrophoresed on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) (Beyotime, Shanghai, China) and then transferred to polyvinylidene fluoride (PVDF) membranes (EpiZyme, Shanghai, China), followed by 5% bovine serum albumin (BSA) (Beyotime, Shanghai, China) to block nonspecific antigens of proteins. The membranes were then incubated with primary antibody (Bax, Abcam, Cambridge, MA, USA, Rabbit, 1:1000; Bcl-2, Abcam, Cambridge, MA, USA, Rabbit, 1:1000; DHCR24, Abcam, Cambridge, MA, USA, Rabbit, 1:1000; PI3K, Abcam, Cambridge, MA, USA, Rabbit, 1:1000; p-PI3K, Abcam, Cambridge, MA, USA, Rabbit, 1:1000; AKT, Abcam, Cambridge, MA, USA, Rabbit, 1:1000; p-AKT, Abcam, Cambridge, MA, USA, Rabbit, 1:1000; GAPDH, Abcam, Cambridge, MA, USA, Rabbit, 1:1000) at 4°C overnight, and then incubated with secondary antibody. Finally, the gel imaging system electrochemiluminescence (ECL) was used for development.
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8

Antioxidant and Cytoprotective Effects

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Anthocyanins were obtained from Extrasynthese (Genay, France). RPMI-1640 media, fetal bovine serum (FBS), and paraquat solution were purchased from Sigma-Aldrich (St. Louis, MO, USA). RIPA, Cell Counting Kit-8 (CCK-8), 2′, 7′-dichlorofluorescin diacetate (DCFH-DA), sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and BCA protein assay kits were purchased from Beyotime Institute of Biotechnology (Haimen, Jiangsu, China). Kits used for lactate dehydrogenase (LDH), methane dicarboxylic aldehyde (MDA), glutathione peroxidase (GPx), and superoxide dismutase (SOD) detection were purchased from the Jiancheng Institute of Bioengineering (Nanjing, China). Trizol was purchased from Invitrogen (Carlsbad, CA) and the FastQuant RT Kit was purchased from TIANGEN (Beijing, China). Antibodies used for Western blot analyses were anti-Bcl-2, anti-Bax, anti-vimentin, anti-TGF-β1, anti-ALK5, and anti-β-actin (Santa Cruz Biotechnology, Santa Cruz, CA, USA); anti-phospho-smad2 (p-smad2) and anti-smad2 (Cell Signaling Technology, Beverly, MA); anti-E-cadherin, anti-α-SMA, and anti-col-I (Abcam, Cambridge, MA, USA); and horseradish peroxidase (HRP)-conjugated antibody (Sigma-Aldrich, St. Louis, MO, USA).
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9

Quantitative Western Blot Analysis of Proteins

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Total protein was isolated from rBMSCs using RIPA lysis buffer (Beyotime) with 1 mM phenylmethanesulfonyl fluoride (PMSF; Beyotime). Nucleoproteins were isolated according to the instructions of a Nuclear and Cytoplasmic Protein Extraction Kit (Beyotime). Then, the protein concentrations were quantified using a BCA kit (Beyotime). Fifteen microliters of each protein sample was separated via sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS–PAGE; Beyotime), and the proteins were then transferred onto a polyvinylidene difluoride (PVDF) membrane (Bio–Rad). After blocking with 5% BSA for 2 h, the membranes were incubated with primary antibodies overnight at 4 °C, followed by incubation with the corresponding secondary antibodies for 2 h after washing three times with TBST. Thereafter, the protein bands were detected with PLUS electrochemiluminescence reagent (Bio–Rad). Finally, the intensity of the protein bands was quantified with ImageJ software (National Institutes of Health, Bethesda, MD, USA) and normalized to the internal control: β-actin for total protein and Lamin B1 for nucleoproteins.
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10

TGR5 Activation and cAMP Signaling

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TCDCA (purity ≥ 98%) and TLCA (purity ≥ 97%) were purchased from Sigma Chemical Co. (St. Louis, MO, USA). INT-777 (purity ≥ 98%) was purchased from MedchemExpress Co. (Princeton, NJ, USA). Sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) was purchased from Beyotime Co. (Beijing, China). pMD19-T vector, Hind restriction endonuclease III (Hind III), restriction endonuclease XbaI, and SYBR® Premix Ex TaqTM were purchased from Takara Co. (Shiga, Japan). pCMV-C-EGFP plasmid and pCMV-Blank plasmid were purchased from Tiangen Co. (Beijing, China). LipofectamineTM 2000 transfection reagent was purchased from Invitrogen Co. (Carlsbad, CA, USA). Sheep anti-rabbit TGR5 antibody, Rabbit anti-goat TGR5 antibody, and Rhodamine-labeled mouse anti-goat antibody were purchased from Cruz Santa Co. (Dallas, TX, USA). Horseradish peroxidase-labeled Goat anti-rabbit antibody was purchased from KPL Co. (Gaithersburg, MD, USA). cAMP ELISA Kit was purchased from Cayman Co. (Ann Arbor, MI, USA). The Bright-GloTM Luciferase Assay Kit was purchased from Promega Co. (Madison, WI, USA). The Nuclear Extract Kit was purchased from Active Motif Co. (Carlsbad, CA, USA). Dulbecco’s Modified Eagle Medium was purchased from Hyclone Co. (Shanghai, China). Fetal bovine serum was purchased from ExCell Co. (Taicang, China). Other reagents were purchased from ExCell Co.
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