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197 protocols using β tubulin

1

Western Blot Analysis of Cellular Proteins

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Cells and tissue samples were lysed in RIPA buffer with PMSF as protease inhibitor (Beyotime, Shanghai, China). Proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and transferred on NC or PVDF membrane (Millipore, Bedford, MA). After blocking with 5% dry milk in TBST for 2 h at room temperature, the membranes were incubated with the primary antibodies against SDHB (1:1000, Epitomics), β-tubulin (1:4000, Epitomics), β-actin (1:500, Abmart), caspase 3 (1:1000, Cell Signalling Technology), Bcl-2 (1:4000, Epitomics), MMP-2 (1:500, Abcam), FAK (1:1000, CST), p-FAK (1:1000, CST), AMPKα (1:1000,CST), p-AMPKα (1:1000, CST), GAPDH (1:4000, Abmart), P38 (1:1000, CST), p-P38 (1:1000, CST), ERK (1:1000, CST), p-ERK (1:1000, CST), HIF-1α (1:1000, Epitomics) in dilution buffer overnight at 4°C. Membranes were washed for three times with TBST, then were incubated with IRDye 800CW conjugated goat (polyclonal) anti-Rabbit IgG or anti-Mouse IgG (1:10000) antibodies for 1 h at room temperature. The expression of specific proteins was detected through the use of Odyssey system following the manufacturer's instructions.
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2

Molecular Signaling Pathway Regulation

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Chemicals, including resveratrol, tBHQ, and 2′,7′-dichlorofluorescin diacetate (DCFH-DA), and alkaline phosphatase- (AP-) conjugated secondary antibody (anti-rabbit IgG) were purchased from Sigma-Aldrich (St. Louis, MO, USA). Primary antibodies against phosphor-Akt (pS473), phosphor-ERK1 (pY204)/ERK2 (pY187), phosphor-JNK1 (pT183)/JNK2 (pT183)/JNK3 (pT221), and β-tubulin were purchased from Epitomics (Burlingame, CA, USA). Antibody against phospho-p38 (Thr 180/Tyr 182) was purchased from Cell Signaling Technology (Danvers, MA, USA), and anti-Nrf2 antibody was purchased from Abcam (Cambridge, Massachusetts, USA). Specific inhibitors, PD98059 (for ERK1/2 signaling), LY294002 (for Akt signaling), SP600125 (for JNK signaling), and SB203580 (for p38 signaling), were obtained from Selleckchem (Houston, TX, USA). Other analytical grade chemicals were purchased from Sangon Biotechnology Co. (Shanghai, China).
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3

Molecular Signaling Pathways Analysis

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Cells were lysed in RIPA buffer (Millipore) supplemented with Complete Protease Inhibitor Cocktail (Roche), 2 mM PMSF, and 0.1% SDS. The protein concentration was measured using the BCA assay kit (Thermo Scientific). Total protein (~30 μg) was separated by 10% SDS-PAGE and then transferred to 0.45 μm nitrocellulose membrane (Millipore). The membrane was blocked with TBST containing 5% non-fat milk, incubated with SIRT3 (Cell Signaling), Akt (Cell Signaling), p-Akt Ser473 (Cell Signaling), c-MYC (Epitomics&Santa Cruz), p-c-MYC(T58) (Epitomics), Ubiquitin (Santa Cruz), β-tubulin (Epitomics), β-actin (Epitomics) at 4°C overnight and then hybridized with appropriate HRP-conjugated secondary antibody at room temperature for 1 h. Protein signals were visualized using ECL detection system (Thermo Scientific).
For immunoprecipitation, 150-500 μg lysates prepared as above were incubated on ice with 4-10 μg of the appropriate antibodies and 20 μl protein G-sepharose beads (Roche) overnight. Immuno-complexes were washed 4-5 times with PBS (Invitrogen) before immunoblotted with the indicated antibodies.
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4

Hippocampal Protein Signaling Pathway Analysis

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The whole hippocampus (ventral and dorsal) was lysed in RIPA buffer containing protease inhibitors and phosphatase inhibitors. Protein concentration was determined colorimetrically by NANODROP 2000 (Thermo Scientific). Protein lysates were separated by 10% SDS-PAGE electrophoresis and were transferred onto polyvinylidenedifluoride (PVDF) membranes. After blocking with 5% BSA for 1 hr, and the following antibodies were used: NR1(Santa Cruz Biotechnology, 5704S, 1 : 500), AKT/p-AKT (Cell Signaling Technology, 9272S, 4058s, 1:500), mTOR/p-mTOR (Cell Signaling Technology, 2972S, 2971S,1:500), p70S6 kinase p70s6k) / p--p70S6K (Cell Signaling Technology, 2708S, 9234S, 1:500), p-4EBP1 (Cell Signaling Technology, 9644S.1:1000), GluR1 (Cell Signaling Technology, 12551S, 1:1000) and β-tubulin (Epitomics, 1879-1, 1:2000). After the blots were incubated with antibodies overnight at 4 °C, they were incubated with horseradish peroxidase- conjugated secondary antibodies for 1 hr. The blots were visualized using the SuperSignal West Pico Chemiluminescent Substrate (Thermo Fisher Scientific Inc.). The resulting data was analyzed statistically using SPSS Statistics 20. All experiments were performed in troplicate. The final data are expressed as a ratio of the relative optical density (ROD) of the protein of interest to the ROD of β-tubulin. A p-value < 0.05 was considered significant.
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5

Immunoblot Analysis of Cellular Proteins

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Cells were lysed on ice for 30 min using RIPA buffer and PMSF (Beyotime, Shanghai, China). Proteins were separated by SDS-PAGE and transferred to a Polyvinylidene Fluoride membrane (Millipore, Bedford, MA). After blocking with 5% dry milk in TBST for 2 h at room temperature, the membranes were incubated with the primary antibodies against human SDHB (1:1000, Epitomics), β-tubulin (1:4000, Epitomics), βactin (1:500, Abmart), ERCC1 (1:400, Abcam), phospho-histone H2A.X (γ-H2A.X, 1:1000, Cell Signaling Technology) in dilution buffer overnight at 4°C. After washing three times with TBST, memmbranes were incubated with IRDye 800CW Conjugated Goat (polyclonal) Anti-Rabbit IgG or Anti-Mouse IgG (1:10000) antibodies for 1 h at room temperature. The expression of speci c proteins was detected through the use of Odyssey system following the manufacturer's instructions.
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6

Inflammatory Cytokine Regulation Analysis

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Lipopolysaccharide was purchased from Sigma-Aldrich (St Louis, Ca). Recombinant mouse IL-4, recombinant mouse IL-6, recombinant mouse IL-1β, recombinant mouse TNF-α, recombinant mouse IL-10, and recombinant mouse TGF-β were purchased from R&D Systems (Minneapolis, MN). Tocilizumab, LY2109761, R-7050, Stattic, Bay 11-7082, and SIS3HCl were purchased from Selleck (Huston, USA). IL-1 receptor antagonist (IL1Ra) was purchased from Make Research Easy (Nanjing, China). Monoclonal mouse anti-β-actin (TA-09) was purchased from Zhongshan Golden Bridge Biotechnology (Beijing, China). Antibodies against OT, OTR, β-tubulin, CD206, F4-80, phospho-STAT3, STAT3, phospho-SMAD2, SMAD2, phospho-SMAD3, SMAD3, p65, and phospho-p65 were purchased from Abcam (Cambridge, UK) and Cell Signaling Technology (Danvers, MA). Secondary antibodies were purchased from Invitrogen Life Technology (Foster City, CA). Mouse ELISA kits were obtained from R&D Systems and CUSABIO (Wuhan, China). All reagents were analytical grade.
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7

Western Blot Analysis of Vascular Factors

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Western blots were performed using standard protocols. Immediately after dissection, twelve hyaloid vascular tissues or retinae of P6 (six pups) were pooled in 100 μl of 1x Laemmli sample buffer and sonicated. After centrifugation, 20 μl of supernatant was loaded on 4 to 20% gradient protein gel (ThermoFisher Scientific). Separated protein bands were transferred to PVDF membrane, and bands were visualized by chemiluminescence (ThermoFisher Scientific). Unprocessed immunoblots are available in Supplementary Fig. 6. Band intensity was measured by ImageJ (NIH). Following antibodies were used for Western blotting: VEGFR2 (Cell Signaling Technology, #9698), phospho-VEGFR2 (Cell Signaling Technology, #2478), β-tubulin (Abcam, ab6046), DAT (Novus, NB300–254), phospho-DAT (ThermoFisher Scientific, PA5–35414), AKT (Cell Signaling Technology, #4691) and phospho-AKT S473 (Cell Signaling Technology, #4060). All antibodies were used at 1:1000 dilution.
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8

Protein Isolation and Western Blot Analysis

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Protein isolation was performed using NP-40 lysis buffer (50 mmol/L Tris-HCl pH 7.5, 150 mmol/L NaCl, 1% NP-40, 0.5% sodium deoxycholate, 1 mmol/L EDTA pH 8 and 1 tablet of protease inhibitor cocktail Roche cOmplete (Roche) and 1 tablet of phosphatase inhibitor PhosSTOP (Roche). A total of 30 μg of protein per sample was separated on NuPAGE 4% to 12% Bis-Tris precast polyacrylamide gels (Novex, Thermo Fisher Scientific), transferred onto iBLOT2 polyvinylidene difluoride membranes (Invitrogen, Thermo Fisher Scientific) then blocked using Odyssey blocking buffer (LiCor). Primary antibodies used in Western blot analysis were cleaved caspase-3 (Asp175 No. 9661, Cell Signaling, Technology), BIMS/EL/L (ALX-804–527, Enzo Life Sciences), BMF (ALX-804–343-C100, Enzo Life Sciences), MCL-1 (5453S, Cell Signaling Technology), phosho-p44/42 MAPK (ERK1/2) Thr202/Thr204 (4370, Cell Signaling Technology), p44/42 MAPK (ERK1/2; 9107, Cell Signaling Technology), β-actin (A5316, Sigma-Aldrich), and β-tubulin (ab6046, Abcam). Secondary antibodies used include IRDye 680RD Goat anti-mouse IgG (H+L), IRDye800CW Goat anti-rabbit IgG (H+L), and IRDye680RD Goat anti-rat IgG (H+L; LiCor). Signal was detected using an Odyssey imaging system (LiCor).
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9

Western Blot Analysis of Cellular Proteins

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Cells were washed twice with cold PBS and scraped in 50 mM Tris HCl pH 8.0, 150 mM NaCl, 1% NP-40, 0.5% sodium deoxycholate and 0.1% SDS supplemented with protease and phosphatase inhibitors (Roche). After centrifugation at 10,000 g supernatants were boiled in Laemmli buffer for 10 min and proteins were resolved by SDS-PAGE. Proteins were subsequently transferred onto PVDF membrane and blocked for 1 hour in TBS containing 0.05% Tween 20 (TBS-T) supplemented with 5% skim milk powder. Membranes were probed overnight at 4°C with antibodies directed against: DICER (1:200, H-212; Santa Cruz Biotechnology), CA9 (1:1000, M75; gift from Dr. Silvia Pastorekova), H3K27me3 (1:20000, 07-449; Upstate), H3 (1:5000, D1H2; Cell Signaling Technology), E-cadherin (1:1000, Cell Signaling Technology), Vimentin (1:500, clone V9; Sigma), β-tubulin (1:20000, Abcam), β-actin (1:20000, Sigma) or eIF4E (1:1000, BD Transduction Laboratories). Bound antibodies were visualized using HRP-linked secondary antibodies (GE Healthcare) and ECL luminescence (Pierce).
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10

Subcellular Protein Extraction and Analysis

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Nuclear and cytoplasmic protein was extracted from cells by suspension in a solution of Buffer A containing 10 mM HEPES pH 7.4, 1.5 mM MgCl2, 10 mM NaCl, 0.1% NP-40 and a cocktail of protease inhibitors (Complete Mini Cocktail, Roche Diagnostics Ltd, Lewes, UK). The cells were lysed on ice for 10 min after which they were passed through a 21 gauge needle to ensure complete plasma membrane lysis. Nuclei were pelleted by centrifugation (12,000 x g at 4°C for 2 min) and the supernatant containing cytoplasmic protein was retained. Nuclei were washed in a solution of Buffer A (as specified above). The nuclei were lysed for 10 min on ice in Buffer A and sonicated for 30 sec to completely disrupt the nuclear membrane. Remaining cell debris was pelleted by centrifugation and the supernatant containing nuclear protein retained. Total protein content was determined by the Bradford protein method using the BCA protein assay kit (Pierce, Cramlington, UK). Protein (30 μg) was loaded onto a Tris-Glycine polyacrylamide gel (10%) and subsequently transferred to a nitrocellulose membrane. The antibodies used for Western blotting were β-tubulin (Abcam 1:1000), HOXD10 (Biorbyt 1:200), POU2F1 (Abcam 1:1000) and TATA-BP (Abcam 1:1000).
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