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18 protocols using ab176560

1

Western Blot Analysis of Autophagy and Inflammatory Markers

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Western blot analysis was performed as described previously[9 (link)]. Briefly, cultured cells were homogenized in a lysis buffer containing a protease inhibitor cocktail. After SDS-PAGE, the proteins on the gel were transferred to a polyvinylidene membrane. Then, the membrane was stained with the desired antibodies. The membrane was visualized with ImmobilonWestern (Millipore, Hayward, CA), and the image was captured with ChemDoc XRS (Bio-Rad, Hercules, CA). Primary antibodies used for Western blotting: microtubule-associated protein 1 light chain 3 (LC3) rabbit polyclonal antibody (PM036; MBL, Nagoya, Japan), p62 mouse monoclonal antibody (ab56416; Abcam, Cambridge, UK), PARP1 rabbit polyclonal antibody (9542S; Cell Signaling Technology, Danvers, MA), phospho-NF-kB p65 rabbit monoclonal antibody (Ser536) (3033S; Cell Signaling Technology), NF-kB p65 rabbit polyclonal antibody (sc-372; Santa Cruz Biotech, Dallas, TX), phosphor-extracellular signal–regulated kinase (ERK) rabbit polyclonal antibody (9101S; Cell Signaling Technology), ERK rabbit monoclonal antibody (4695S; Cell Signaling Technology), tubulin rabbit monoclonal antibody (ab176560; Abcam). Goat anti-rabbit IgG-HRP (sc-2030; Santa Cruz) or goat anti-mouse IgG-HRP (sc-2005; Santa Cruz) were used as secondary antibodies.
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2

Radiolabeling and Immunoblotting Protocol

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All chemicals and solvents were obtained at analytical grade from Sigma‐Aldrich (Dorset, UK), Merck (Hertfordshire, UK), CheMatech (Dijon, France), or Macrocyclics (Dallas, TX) and were used without further purification. F3 peptide (KDEPQRRSARLSAKPAPPKPEPKPKKAPAKK, MW = 3432 g/mol) was obtained from Cambridge Peptides (Cambridge, UK). Size and purity were confirmed by reverse phase high‐performance liquid chromatography (HPLC) and mass spectroscopy. Bacterial transglutaminase was obtained from Zedira (Darmstadt, Germany). No‐carrier‐added (NCA) fluorine‐18 dissolved in [18O]H2O was provided by PETNET Solutions (Middlesex, UK). [111In]InCl3 was provided by Perkin Elmer (Waltham, MA). Antibodies against nucleolin (ab129200), β‐actin (ab8227), H2AZ (ab4174), β‐integrin (ab179471), and α‐tubulin (ab176560) were obtained from Abcam (Cambridge, UK); anti‐PARP‐1 antibody F‐2 was obtained from Santa Cruz Biotechnology, Inc. (Dallas, TX); and all other antibodies were obtained from Invitrogen (Paisley, UK).
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3

Protein Extraction and Western Blot Analysis

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Cytoplasmic and nuclear protein were extracted from 5 × 106 OCI-AML3 cells exposed to OTX015 (MK-8628), JQ1, ATO + ATRA or 0.1% DMSO with NE-PER Nuclear and Cytoplasmic kit (#78833, Life Technologies, Courtaboeuf, France). Proteins thus obtained were concentrated with Amicon Ultra centrifugal filters, Ultracel 30 K and 10 K (#UFC503096 and #UFC501096, Merck Millipore, St. Quentin Fallavier, France). Thirty microgrammes of cytoplasmic proteins and 5–10 µg of nuclear proteins were loaded on SDS-polyacrylamide gels using 4–15% gradient gels (Bio-Rad, Marnes-La-Coquette, France) and transferred to nitrocellulose membranes using a Mini Trans-Blot Electrophoretic Transfer cell (Bio-Rad, Marnes-La-Coquette, France). Membranes were blocked with LI-COR blocking buffer and incubated with the primary antibody overnight at 4 °C: anti-NPM1m (#ab65816, Abcam, Paris, France), anti-NPM1total (#H00004869-M01, CliniSciences, Nanterre, France), anti-BRD4 (#ab128874, Abcam, Paris, France), anti-tubulin (#ab176560, Abcam, Paris, France), or anti-lamin (#ab16048, Abcam, Paris, France). Secondary antibodies were goat anti rabbit HRP or goat anti mouse HRP (Bio-Rad, Marnes-La-Coquette, France), incubated for 1 h at room temperature. Bands were visualized using the ChemiDoc Touch (Bio-Rad, Marnes-La-Coquette, France).
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4

Western Blot Analysis of Protein Targets

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Cell lines or tumor tissues were harvested and lysed in RIPA buffer (1% NP 40, 0.5% sodium deoxycholate, 0.1% SDS, 10 ng/ml PMSF, 0.03% aprotinin, and 1 μM sodium orthovanadate) on ice for 30 min. After centrifugation for 15 min at 14,000 rpm, the supernatants were collected, and the protein concentration was quantified by using Bradford assay. The proteins were separated on 12% SDS-PAGE gels and transferred to polyvinylidene difluoride membranes. The membranes were blocked with 5% skim milk and incubated with primary antibodies, such as MLX (12042-1-AP, Proteintech), β-actin (81115-1-RR, Proteintech), TRC/CD71 (66180-1-Ig, Proteintech), SLC40A1/FPN1 (26601-1-AP, Proteintech), Transferrin (66171-1-Ig, Proteintech), FTH1 (3998S, Cell Signaling Technology), cleaved Capase-3 (9661S, Cell Signaling Technology), SLC7A11(12691S, Cell Signaling Technology), Tubulin (ab176560, Abcam) and 4-Hydroxynonenal (ab46545, Abcam), Caspase-3 (ab184787, Abcam), and corresponding horseradish peroxidase-conjugated secondary antibodies were used against each primary antibody. Proteins were detected and filmed by using chemiluminescent detection reagents.
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5

Analysis of Macrophage Phenotypic Markers

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To analyze the macrophage phenotypic shape markers arginase-1 and iNOS, the cells cultured on each nanofiber membrane sample were separated by 0.25 % trypsin and transferred to the lysis buffer containing 1 % benzenesulfonyl fluoride; after 30 min of complete lysis at 4 °C, protein samples were collected by centrifugation at 25,000 rpm for 15 min, and the total protein concentration was measured by commercial kits. For Western blotting, the main antibodies used were anti-arginase-1 (1:1000, PA5-85267, Gibco), anti iNOS (1:1000, PA3-030a, Gibco), and anti-α-tubulin (1:1000, ab176560, Abcam), the subsequent procedures were performed as described previously [26 (link)–28 (link)].
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6

Protein Expression Analysis Workflow

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Cells were lysed in 300 μl of NET-2 buffer (150 mM NaCl, 0.05% NP-40, 50 mM Tris, pH 7.5), supplemented with cOmplete Protease Inhibitor Cocktail (Sigma Aldrich) and 10 mM β-glycerophosphate (Fluka BioChemica). Lysates were sonicated on ice for 30 s (three pulses of 10 s; 20 s intervals) at 20% amplitude (Branson W-450 D) and cleared by centrifugation. Protein concentrations were measured using Quick Start Bradford 1× Dye Reagent (Bio-Rad) on a NanoDrop2000 (Thermo Fisher Scientific). A 20–30 μg aliquot of protein was separated by sodium dodecylsulfate (SDS)–polyacrylamide gel electrophoresis (PAGE) either on 8% stain-free gels (Bio-Rad) or on NuPAGE 4–12% Bis-Tris gels (Thermo Fisher Scientific) and transferred onto nylon membranes (0.1 μm pore size, EMD Millipore). Transfer and equal loading were evaluated by activation of stain-free gels by UV light. Membranes were probed with the following antibodies and dilutions in Tris-buffered saline/Tween (TBST): 1:3 α-mouse mAb104 (CRL_2067; ATCC), 1:100 α-rabbit HIF1α (NB100-134; Novus Biologicals), 1:100 α-rabbit SRSF6 (LS-C29032711; LifeSpan Biosciences), 1:1000 α-rabbit SRSF4 (NBP2-04144, Novus Biologicals), α-mouse BNIP3 (ab10433, Abcam) and α-rabbit alpha-tubulin antibody (ab176560; Abcam). Image acquisition and quantification were performed using the ImageLab software (Bio-Rad).
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7

Western Blot Analysis of TWIST1

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Whole cell extracts (40-50 µg) from cells or tissues were separated by SDS-PAGE and then transferred to polyvinylidene difluoride membranes (PVDF; Bio-Rad, Hercules, CA, USA). The membranes were blocked and then probed with antibodies against TWIST1 (ab50887) and anti-alpha tubulin (ab176560) as a loading control (Abcam, Cambridge, MA, USA). After washing, the blots were incubated with horseradish peroxidase-conjugated secondary antibodies.
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8

Western Blot Analysis of Bladder Cancer Cells

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The transfected J82 and T24 cells were lysed using protein inhibitor modified RIPA lysate (Thermo Fisher) on ice, and the total cell protein was extracted. After accurate loading, electrophoresis separation was performed on a 10% SDS-PAGE gel, and then transferred to a superior PVDF membrane. The PVDF membrane was blocked with skim milk (BD) for 2 h. The following primary antibodies were added and incubated overnight at 4 °C, anti-SHMT2(1:1,000, ab224428; Abcam, Cambridge, UK), anti-Tubulin(1:10,000, ab176560; Abcam, Cambridge, UK), anti-MMP7(1:1,000, ab205525; Abcam, Cambridge, UK), anti-Integrin β-4(1:1,000, ab182120; Abcam, Cambridge, UK), anti-Laminin β-4(1:500, Sc-130540; Santa Cruz, CA, USA), anti-SHMT1(1:800, Cat.14149–1-AP; Proteintech, Wuhan, China), anti-E-cadherin (1:2,000, Cat.60335–1-Ig; Proteintech, Wuhan, China), anti-N-cadherin (1:2,000, Cat.66219–1-Ig; Proteintech, Wuhan, China), anti-MMP2 (1:2,000, Cat.66366–1-Ig; Proteintech, Wuhan, China), anti-GAPDH (1:10,000, Cat.60004–1-Ig; Proteintech, Wuhan, China). The membrane was washed the next day and secondary antibodies were added and incubated for 30 min. After washing, the membrane was treated with ECL chemiluminescence reagent for 1 min and finally imaged using a fluorescence imaging system. The gray value of protein bands was analyzed using Image J software and the experimental data were recorded.
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9

Protein Expression Analysis of NLRP3 Inflammasome

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Total protein of cells and heart tissues were extracted and quantified with BCA Protein Assay kit (Beyotime, Shanghai, China), separated by SDS-PAGE, and then transferred to a PVDF membrane. Each membrane was blocked for 1.5 h at room temperature in 5% non-fat milk, followed by incubation overnight at 4°C with the primary antibodies against NLRP3 (1:1000, abcam, ab263899, United Kingdom), apoptosis associated speck like protein containing a CARD (ASC) (1:500, abcam, ab180799, United Kingdom), Caspase-1 (1:1000, Immunoway,YT5743, United States), cleaved-Caspase-1 (1:1000, abcam, ab179515 United States), YAP1 (1:2000, proteintech, 66900-1-Ig, China), phosphor-YAP1 (ser127) (1:1000, cell signaling technology, 13008s, United States), YAP1 (1:2000, proteintech, 66900-1-Ig, China), phosphor-YAP1 (ser127), LATS (1:1000, proteintech, 17049-1-AP, China), phosphor-LATS1 (Thr1079/1041) (1:1000, immunoway, YP1222, United States), and α-tubulin (1:2000, abcam, ab176560, United Kingdom). The membrence then incubated with the horseradish peroxidase (HRP)-labeled goat anti-rabbit and goat anti-mouse secondary antibodies for 1 h at room temperature. And the expression of protiens was visualized using enhanced chemilumi-nescence reagents (biosharp, BL520A, China).
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10

Antibody Resources for Protein Analysis

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Antibodies against CK2 (ab10466), tubulin (ab176560), AKT1 pSer129 (ab133458) and CDC37 pSer13 (ab108360) were from Abcam. Antibodies against GAPDH (#2118), Lamin A/C (#2032), UBE2N (#6999), CDC37 (#3618) and AKT1 (#9272) were from Cell Signaling Technologies. The antibody against 53BP1 was from Bethyl Laboratories. The antibody against ubiquitin was from Dako (Z0458) and that against HA was from Roche (12CA5). HRP-conjugated antibodies against FLAG (#A8592) and HA (#12013819001) were from Sigma and Roche, respectively. Human recombinant full length OTUB1, ALK5 (amino acids 142-172) polypeptide, and pSer16-OTUB1 (amino acids 10-22, KQEPLGSDSEGVN) polypeptide were used as immunogens to generate the respective antibodies. All recombinant proteins, plasmids and antibodies generated for the present study are available on request and described in further detail on our reagents website (https://mrcppureagents.dundee.ac.uk/).
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