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1

Influenza Virus Internalization Assay

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A549 cells were grown in 6-well plates to 90% confluence and then infected with AH05 (H5N1) virus (MOI = 5) for 1 h on ice at 4°C. The infected cells were washed five times with ice-cold PBS (pH 7.2) or PBS-HCl (pH 1.3). Afterwards, the cells were lysed with SDS-PAGE loading buffer (Solarbio, Beijing, China) and then subjected to Western blotting with a rabbit anti-NP pAb.
A549 cells in 6-well plates were treated with siRNA targeting FFAR2 or AP2B1 or with scrambled siRNA (30 nM) for 48 h and then infected with AH05 (H5N1) virus (MOI = 5) on ice at 4°C for 1 h, followed by a culture temperature shift to 37°C for 30 min to allow for internalization. The cells were then washed five times with ice-cold PBS-HCl (pH 1.3) to remove the attached but not-yet-internalized virions and then subjected to Western blotting with a rabbit anti-NP pAb.
A549 cells were grown in 6-well plates to 90% confluence and then treated with DMSO, 4-CMTB (100 μM), or Cmp58 (10 μM) for 3 h at 37°C prior to infection with AH05 (H5N1) virus (MOI = 5) at 37°C. The cells were washed five times with ice-cold PBS-HCl (pH 1.3) at the indicated time points p.i. to remove the attached but not-yet-internalized virions and then subjected to Western blotting with a rabbit anti-NP pAb.
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2

Western Blot Analysis of Prostate Proteins

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The cells were washed with ice-cold PBS three times and lysed with RIPA lysis buffer (Sangon Biotech, China) with a protease inhibitors cocktail (Roche, China). The total protein content in the supernatant was measured by the BCA protein assay kit (Sangon Biotech, China) according to the manufacturer’s instruction. The samples were boiled with SDS-PAGE loading buffer (Solarbio, China). Twenty micrograms of protein was added to each lane, separated in 10% SDS-PAGE, and transferred to polyvinylidene fluoride (PVDF) membranes (Millipore, MA, USA) in a Trans-Blot apparatus (Tanon, China). 5% BSA diluted in TBS-T (0.05% Tween 20 in TBS) was used to block the membranes, and the primary antibodies with optimized concentrations, including AR (1:1000, ab108341, Abcam, USA), Actin (1:1000, D191048, Sangon Biotech, China), PSA (1:1000, 10679, Proteintech, China), were added to the membranes overnight at 4 °C. The membranes were incubated with the corresponding secondary antibodies conjugated with HRP (1:10000, D110011, Sangon Biotech, China) for 1 h at room temperature, and the bands were visualized by an enhanced chemiluminescence detection system.
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3

Protein Extraction and Western Blot Analysis

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The total proteins were extracted from cells with radioimmunoprecipitation assay (RIPA) lysis buffer mixed with PMSF, protein inhibitors, and phosphatase inhibitors (Beyotime, China) and denatured by SDS‐PAGE loading buffer (Solarbio, China). An equal quantity of protein was separated using smartPAGE™ precast protein gel plus (4%–20%, Bis‐Tris) (Smart‐Lifesciences, China) in MOPS Running Buffer (Smart‐Lifesciences, China) and transferred to polyvinylidene difluoride (PVDF) membranes (Millipore, USA) in NcmBlot Rapid Transfer Buffer (NCM Biotech, China). The membranes were blocked with 5% nonfat dry milk (Beyotime, China) for 1.5 h and then incubated with primary antibodies: METTL14 polyclonal antibody (26158‐1‐AP, 1:1000, Proteintech, China), p21 polyclonal antibody (10355‐1‐AP, 1:1000, Proteintech, China), p53 polyclonal antibody (10442‐1‐AP, 1:1000, Proteintech, China), FTO polyclonal antibody (27226‐1‐AP, 1:1000, Proteintech, China), collagen type I polyclonal antibody (14695‐1‐AP, 1:1000, Proteintech, China), ERRFI1 polyclonal antibody (11630‐1‐AP, 1:1000, Proteintech, China), and GAPDH polyclonal antibody (10494‐1‐AP, 1:20000, Proteintech, China). Proteins were then incubated by anti‐rabbit IgG, HRP‐linked antibody #7074 (CST, USA) for 1.5 h and detected by an enhanced chemiluminescence system (ECL) reagent (Biosharp, China).
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4

Western Blot Analysis of Cell Signaling

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Cells were washed once with ice-cold PBS and lysed in 100 µl RIPA lysis buffer (Solarbio, #R0010) with PMSF and Cocktail. Lysate was extracted with SDS-PAGE loading buffer (Solarbio, #P1040) for 5 min at 100°C. Proteins were transferred to Immobilon-FL 0.45 µm PVDF membranes (Millipore) and subjected to immunoblot analysis with following antibodies:PD-L1 (1:1000, CST, #13684 S), phospho-ROS1 (1:1000, CST, #3078 S), ROS1 (1:1000, CST, #3266 S), p-ERK (1:1000, CST, #9106 S), ERK (1:1000, CST, #4695 S), p-STAT3(1:1000, CST, #9145 S), STAT3 (1:1000, CST, #9139 S), p-AKT (1:1000, CST, #4060 S) and AKT (1:1000, CST, #4685), β-actin (1:5000, ZSGB-BIO, #TA-09). Bio-Rad ChemiDocTM MP imaging system or LI-COR Odyssey Platform was used for western blot detection with either HRP-conjugated or IR dye secondary antibodies, respectively. Flow cytometry antibodies for PD-L1 were purchased from BD Biosciences, conjugated with PE-CY7 (BD, #558017) or APC (BD, #563741).
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5

CIDEC Immunoprecipitation from Mouse Intestine

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Small intestine tissue was collected from WT mice (no flox). Intestinal protein supernatants were prepared and the protein concentration was assayed as described above. The supernatants were immunoprecipitated with a polyclonal CIDEC antibody (Cloud-Clone Corp; Wuhan, China) following the manufacturer's protocol. Briefly, 3 mg protein supernatant samples were precleared by IgG and arotein L-agarose (Santa Cruz Biotechnology; Dallas, TX, USA) for 30 min, incubated with 2 mg of primary antibody for 1h and then incubated with protein L-agarose at 4 °C overnight (16 h). The bound proteins were washed twice with prechilled RIPA and eluted by boiling in Sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) loading buffer (Solarbio; Beijing, China). The resulting proteins were assayed by SDS-PAGE and sent to APTBIO (Shanghai, China) for mass spectrum analysis.
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6

Comprehensive Analysis of Apoptosis Pathway Proteins

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Antibodies to PCNA, Bax, Bcl-2, Akt, p-AKT, PI3K, p-PI3K, GFP, and PI3K/AKT inhibitor LY294002 were purchased from Cell Signaling Technology (Beverly, USA). GAPDH was obtained from Shanghai Weiao. Dulbecco’s Modified Eagle’s Medium (DMEM), RPMI 1640 Medium, Fetal bovine serum and 0.25% Trypsin-EDTA were purchased from Gibco (Grand Island, NY, USA). SDS-PAGE loading buffer was purchased from Beijing Solarbio. Secondary antibodies and DAB Substrate Kit were purchased from Zhongshan Goldenbridge (Beijing, China). RIPA and PMSF were obtained from Beyotime Biotechnology. TUNEL Assay was from Thermoscientific (Waltham, MA, USA). ELISA kit for human RAGE was from R&D system. Transfer Membranes (PVDF) was from Merck Millipore (Bedford, Massachusetts, USA). Cell counting kit 8 (CCK-8) kit was purchased from BestBio Science (Beijing, China). All other chemicals were obtained from commercially available.
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7

Western Blot Analysis of Protein Expression

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The supernatant (4 μg/μL) mixed with a certain proportion of 5 ×  and 1 ×  SDS-PAGE loading buffer (Solarbio, China) was boiled at 95°C for 10 min. Equal amounts of protein (50 μg/20 μL) were separated by 10% SDS-PAGE (SDS-PAGE Gel Kit, Solarbio Life Sciences, China). Proteins were electrophoretically transferred to polyvinylidene difluoride membranes (Bio-Rad, Richmond, USA), which were then blotted with an antibody against ATP synthase subunit epsilon (ATP5E) (ThermoFisher, USA) diluted 1 : 500, voltage-dependent calcium channel subunit alpha-2/delta-1 (CACNA2D1) (Abcam, Hong Kong) diluted 1 : 10000, glutathione peroxidase 3 (Gpx-3) (Santa, USA) diluted 1 : 2000, and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (Immunoway, USA) diluted 1 : 20000. A secondary antibody (Abcam, Hong Kong) was used to detect the primary antibody. Anti-beta actin antibody (Immunoway, USA) and secondary antibody (Abcam, Hong Kong) were used as references. Finally, chemiluminescence analysis, development, and fixation were carried out. Band signals were detected using an iBright CL750 western blot imaging system (ThermoFisher, USA) and analyzed using iBright Software (ThermoFisher, USA).
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8

Protein Extraction and Western Blot Analysis

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The proteins of GMEC were harvested using RIPA lysis buffer with protease inhibitor and phosphatase inhibitor (Thermo Fisher Scientific, Waltham, MA, USA). Protein quantification was performed using the BCA Protein Assay Kit (Solarbio, Beijing, China), and the same amount of protein was heated with SDS-PAGE loading buffer (Solarbio, Beijing, China) at 98 °C for 10 min to detect specific protein expression. Antibodies specific for MAPK (Cell Signaling Technology, Danvers, MA, 9102, USA), phosphorylated-MAPK (Cell Signaling Technology, Danvers, MA, 4376, USA), mTOR (Boster Biological Technology, Pleasanton, CA, BM4182, USA), p-mTOR (Boster Biological Technology, Pleasanton, CA, BM4840, USA), STAT5 (Cell Signaling Technology, Danvers, MA, 94205, USA), p-STAT5 (Cell Signaling Technology, Danvers, MA, 9359, USA), STC1 (Boster, ba2983-2, Wuhan, China), MMP1 (BBI, D220093, Shanghai, China), and β-actin (Beyotime, AA128, Shanghai, China) were applied.
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9

Western Blot Analysis of Sirt1 in MSCs

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The total protein of the MSCs was collected on ice using SDS–PAGE loading buffer (Solarbio, Beijing, China) supplemented with a protease inhibitor cocktail or phosphatase inhibitor cocktail (Roche, Branchburg, NJ, USA), followed by boiling for 5 min at 100 °C, for denaturation. The protein aliquots were separated by 10% v/v SDS–PAGE and electroblotted onto PVDF membranes (Millipore, Billerica, MA, USA). The membranes were blocked with tris-buffered saline (TBS) containing 0.1% tween 20 (TBST) and 5% v/v non-fat milk, for 1 h, at room temperature. Antibodies against Sirt1 (Cell Signaling Technology, Danvers, MA, USA), and β-actin (ZSGB-BIO, Beijing, China) were used according to the manufacturers’ instructions. The incubation was performed overnight at 4 °C. The membrane was then washed three times with TBST and incubated with horseradish peroxidase-conjugated antibody (ZSGB-BIO, Beijing, China), for 1 h at room temperature. The target proteins’ expression was visualized using an enhanced electrogenerated chemiluminescence (ECL) system (VersaDoc, Bio-Rad, Hercules, CA, USA). The expression of Sirt1 was normalized to the expression of β-actin.
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10

Western Blot Analysis of ZNF667-AS1 Expression

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Protein was extracted from pcDNA3.1 or pcDNA3.1-ZNF667-AS1 transfected AMC-HN-8 or TU177 cells using RIPA lysis buffer added with PMSF (Solarbio, China) and protease inhibitor cocktail (Promega, USA), and followed by ultrasonication (Thermo FB120, USA). The protein concentration was determined using the BCA Protein Assay Kit (Generay, China). Protein lysates were mixed with SDS-PAGE loading buffer (Solarbio, China) and heated at 99 °C for 5 min. Twenty ug of protein was separated by SDS-PAGE and transferred onto PVDF membranes (Bio-Rad, USA). The transferred membranes were blocked with 5% skim milk (BD, USA) at room temperature for 2 h. Blots were incubated with Rabbit anti-human ZNF667 polyclonal antibody (Gene Tex, USA, 1:1000) or GAPDH (Proteintech, USA, 1:5000) overnight at 4 °C, and then incubated with horseradish peroxidase- conjugated secondary antibody at room temperature for 2 h. The band was visualized with enhanced chemiluminescence (ECL) detection reagents (vazyme, China) using ChemiDoc™ XRS+ (Bio-Rad, USA).
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