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29 protocols using a9169

1

Western Blot Analysis of Protein Targets

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Proteins were extracted from PC-3 cells with ice-cold RIPA (Radio Immuno-Precipitation Assay) lysis buffer supplemented with protease inhibitor cocktail (11873580001, Roche), then homogenized in a dounce homogenizer for 1 h and centrifuged at 13,400 rcf at 4 °C for 10 min. The supernatants were collected and boiled with 6x sample buffer at 95 °C for 5 min. The samples were separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis and transferred to nitrocellulose membranes using wet transfer or the semi-dry iBlot Transfer System (Invitrogen, Life Technologies). The membranes were blocked with 5% non-fat dry milk in PBS-T for 1 h, then incubated with either anti-CEBPB (Abcam 18F8, 1:1000 dilution), anti-AR (Cell Signaling 5153 S, 1:1000 dilution), anti-c-Myc (Santa Cruz N262,1:1000), anti-GAPDH (Santa Cruz Biotechnology, sc-322330 dilution) or anti-beta-Tubulin (Santa Cruz Biotechnology 3F3-G2, 1:8000 dilution) antibody in 1% non-fat dry milk in PBS-T overnight at 4 °C. Membranes were then incubated with secondary goat anti-mouse (Santa Cruz Biotechnology A9044, 1:10000) or goat anti-rabbit antibodies (Sigma-Aldrich A9169, 1:12,000) for 1 h at room temperature. Detection was achieved using the ECL Select detection reagent (Amersham, GE Health Care) with the ChemiDoc XRS + System (BioRad) (Supplementary Figs. 19 and 20).
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2

Antibody Characterization for Retinal Protein Analysis

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Primary antibodies used were mouse-anti-NDPK-B (MC-412, Kamiya, Seattle, WA, USA, 1:1000), rabbit-anti-NDPK-A (sc-343, Santa Cruz, Heidelberg, Germany, 1:500; detects both NDPK-A and NDPK-B in mouse retinae), mouse-anti-Ang-2 (sc-74403, Santa Cruz, Heidelberg, Germany, 1:500), mouse-anti-O-GlcNAc (ab-2739, Abcam, Cambridge, UK, 1:1000), rabbit-anti-OGA (SAB4200267, Sigma, Munich, Germany, 1:1000), rabbit-anti-OGT (O-6264, Sigma, Munich, Germany, 1:1000), rabbit-anti-N1-phosphohistidine (MABS1330, Millipore, Darmstadt, Germany, 1:1000), mouse-anti-γ-tubulin (T6557, Sigma-Aldrich, Munich, Germany, 1:2000), rabbit-anti-GFAT (obtained in cooperation with Weigert, Tübingen), and sheep-anti-pGFAT (MRC-PPU s343c) for immunoblotting. The secondary antibodies used were rabbit anti-mouse peroxidase (A9044, Sigma-Aldrich, Munich, Germany, 1:20,000), goat-anti-rabbit peroxidase (A9169, Sigma-Aldrich, Munich, Germany, 1:40,000), and donkey-anti-sheep peroxidase (Sigma-Aldrich). qPCR primers were obtained from Applied Biosystems, ThermoFischer: GFAT Hs00899865_m1, OGA Hs00201970_m1, OGT Hs00269228_m1, and 18S Hs03003631_g1. Gelatin from porcine skin (48720, Fluka, Bucharest, Romania) was used as a 1% solution in PBS. Thiamet G (TMG; SML0244, Sigma-Aldrich, Germany) treatment was given at 10 µM for 24 h.
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3

Western Blot Protein Detection Protocol

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Whole cell extracts were isolated as previously described (52 (link)) and normalized with a Lowry Protein Assay (BioRad, Hercules, CA, USA). Proteins were electrophoresed (on 8% or 10% gels) and transferred to polyvinylidene difluoride (PVDF) membranes followed by a 1 hour blocking incubation at room temperature in 5% milk in Tris-buffered saline with 0.1% tween 20 (TBST). Membranes were then incubated in primary antibody overnight at 4°C. Primary antibodies against the following proteins were used: NOTCH1 (D6F11) (1:1000, Cell Signaling Technologies #4380, Danvers, MA, USA), phospho-Smad3 (1:500, Cell Signaling Technologies, #9520S), β-Actin (1:10,0000, Sigma-Aldrich, #A5316), β-Tubulin (1:1000, Sigma-Aldrich #T4026), and NEDD4L (1:1000, Bethyl Laboratories Inc. #A302-513A, Montgomery, TX, USA). Membranes were then washed in TBST and incubated for 1 hour at room temperature in HRP-anti-mouse (1:10,000, Sigma-Aldrich #A9044) or HRP-anti-rabbit (1:10,000, Sigma-Aldrich #A9169) secondary antibodies. All western blots in the manuscript were replicated in the laboratory at minimum three times, and representative blots are shown.
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4

Hippocampal Tissue Western Blotting

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Western blotting was conducted according to our previous descriptions (Li et al., 2018b (link)). Briefly, hippocampal tissues were lysed in high KCl lysis buffer containing 10 mM Tris–HCl, pH 8.0, 140 mM NaCl, 300 mM KCl, 1 mM EDTA, 0.5% Triton X-100, and 0.5% sodium deoxycholate with 1 mM phenylmethylsulfonyl fluoride (Roche, United Kingdom). The supernatant was quantified using a commercial BCA kit (Beyotime Biotechnology Institute, China). Protein samples were separated by SDS-polyacrylamide gels (SDS-PAGE) and transferred electrophoretically to polyvinylidene fluoride membranes. After blocking, the membranes were incubated with 4-hydroxynonenal (4-HNE) (Mouse, 39–122 KDa, MAB3249, 1 μg/ml, Novus, United Kingdom), GPX4 (Rabbit, 22 kDa, ab125066, 1:5000, Abcam, United Kingdom) and β-actin (Mouse, 43 kDa, A5441, 1:10000, Sigma-Aldrich, United States) overnight. The next day, after washing, the membranes were then incubated with secondary IgG goat anti-rabbit (A9169, 1:10000, Sigma-Aldrich, United States) or rabbit anti-mouse antibody (A9044, 1:10000, Sigma-Aldrich, United States). Immunodetection was performed using an enhanced chemiluminescence kit and the intensity of protein bands was analyzed by Quantity One software (BioRad, United States).
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5

Western Blot Analysis of Protein Targets

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Protein extraction from the cells was achieved using Triton lysis buffer supplemented with protease and phosphatase inhibitor mixtures (Sigma). Cell lysates were loaded with Laemmli buffer, centrifuged for 10 min, and boiled for 5 min. Proteins were separated by SDS-PAGE using 10% SDS-polyacrylamide gel and transferred in a wet condition onto a nitrocellulose membrane (Amersham Biosciences). After blocking with 5% nonfat dry milk, proteins were labeled overnight with primary antibodies as follows: goat anti-NRX (R&D Systems, AF5719; dilution 1:2000); rabbit anti-DVL2 (Cell Signaling, 3216; dilution 1:500); and rabbit anti-GAPDH (Santa Cruz Biotechnology, sc-25778; dilution 1:800) used as stable housekeeping protein. Proteins were probed for 1 h with HRP-conjugated secondary antibodies as follows: anti-goat (Santa Cruz Biotechnology, sc-2020; dilution 1:50,000) and anti-rabbit (Sigma, A9169; dilution 1:80,000). Signals were detected with ECL Western blot detection reagent (GE Healthcare) and quantified with Fiji/ImageJ. Relative signal intensities were normalized to GAPDH.
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6

Western Blot Analysis of Circadian Proteins

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Proteins were separated by SDS-PAGE and transferred onto nitrocellulose membranes. Membranes were incubated with anti-PER2 antibody (Beckton-Dickinson, GP81620-050) 1:1000, anti-p53 antibody (Oncogene, OP03) 1:1000, or anti-actin antibody (Sigma, A5060) 1:1000 (all diluted in blocking buffer) at 4°C over night. They were washed and subsequently incubated with appropriate HRP-conjugated secondary antibodies (anti-rabbit for actin, anti-mouse for PER2 and p53; both Sigma, A9169 and A9044) for 1 h at RT. Detection was performed using the Western blotting detection reagents kit (Amersham Biosciences, 1059243) according to manufacturer’s instructions. Membranes were exposed on Hyperfilm (Amersham Biosciences, RPN1678K). For quantitative analysis, bands were quantified (QuantityOne 3.0, Biorad), and band intensity was normalized to actin.
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7

Western Blot Analysis of EGFP Expression

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Cells were lysed with 1% Triton X-100 (Sigma) and then subjected to sodium dodecyl sulfate polyacrylamide gel electrophoresis, after which proteins were transferred to the polyvinylidene difluoride membrane (Millipore). EGFP primary antibody (ab32146; Abcam) and secondary antibody (A9169; Sigma) were used to detect EGFP, while beta-actin primary antibody (A1978; Sigma) and secondary antibody (A9044; Sigma) were used to detect beta-actin as a loading control. An ECL Chemiluminescent Substrate Reagent Kit (Invitrogen) was used to detect blots of proteins.
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8

Native and SDS-PAGE Protein Analysis

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Samples destined for Native-PAGE analysis were combined with native sample buffer (50 mM Tris-HCl, pH 7.4, 10% glycerol, 0.0014% xylene cyanol at final concentration) and loaded onto polyacrylamide gels [90 mM Tris-borate, pH 8.35, 5 mM MgCl2, 0.5 mM ethylenediaminetetraacetic acid (EDTA), 2.5% sucrose] with 3% stacking and 4% resolving portions. Electrophoresis was performed with native running buffer (90 mM Tris-borate, pH 8.35, 5 mM MgCl2, 0.5 mM EDTA) at 100 V for 3 h on ice. Samples prepared with 20 mM ATP were separated using gels and running buffer containing 1 mM ATP. Samples intended for SDS-PAGE analysis were combined with Laemmli sample buffer [39 (link)] and resolved on 12% gels. Where necessary, gels were stained with Coomassie Brilliant Blue R-250 or silver nitrate [13 (link)]. Alternatively, proteins resolved by Native-PAGE or SDS-PAGE were transferred onto nitrocellulose membrane (PALL BioTrace™; 66,485) and immunoblotted with specific antibodies. Antibodies used in this study include anti-FLAG (Sigma; F1804), anti-PBA1 (Abcam; ab98861), anti-RPN1 (Abcam; ab98865), anti-HSP70 (Agrisera; AS08 371), anti-PA200 (Agrisera; AS19 4269), goat anti-mouse conjugated to horseradish peroxidase (HRP) (Cell Signaling; 7076S), and goat anti-rabbit conjugated to HRP (Sigma; A9169). Chemiluminescent signals were quantified using ImageJ (https://imagej.nih.gov/ij).
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9

Darifenacin Modulates MAPK and PI3K Signaling

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Cells were pretreated with darifenacin (0.1, 1 and 10 µM) for 60 min, followed by addition of ACh (10 µM) for 5 min. Following treatment with ACh, darifenacin or both, cells were lysed using radioimmunoprecipitation assay lysis buffer (Thermo Fisher Scientific) containing phosphatase and protease inhibitors. Protein concentration was quantified by a Quantipro BCA protein assay kit (Sigma-Aldrich) according to the manufacturer’s protocol. Cell extracts were separated by polyacrylamide gel electrophoresis and blotted on polyvinylidene fluoride membranes (Perkin Elmer, Boston, MA, USA). For immune detection, the following primary antibodies were used: anti-p38 (8690), anti-phospho-p38 (4511), anti-ERK1/2 (4695), anti-phospho-ERK1/2 (4370), anti-Akt (pan, 4685), anti-phospho-Akt (pan, 9018), anti-Src (2109S), anti-phospho-Src (6943S; all antibodies 1:1000, Cell Signaling, Leiden, Netherlands) and anti-β-actin (A5441, Sigma-Aldrich). Bound antibodies were visualized by luminescence imaging (Fusion FX, Vilber, Marne-la-Vallée, France) using peroxidase-conjugated secondary antibodies (A9169 and A9044, Sigma-Aldrich) and a chemiluminescent substrate system (SuperSignal West Pico PLUS, Thermo Fisher Scientific). Densitometric quantification was carried out with Image J. β-actin served as internal loading control.
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10

Sphingolipid Pathway Modulation

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Chemicals applied to target sphingolipid pathways were: DL-PDMP (Cayman), an inhibitor for glucosylceramide synthase (UGCG); myriocin (Sigma-Aldrich), an inhibitor for serine palmitoyltransferase; fumonisin B1 (Biomol), an inhibitor for ceramide synthase; altenusin (Enzo), an inhibitor for neutral sphingomyelinases. C8-ceramide (Biomol) is a cell-permeable analog of ceramides. Taxol (TOCRIS) binds to β-tubulin and causes cell cycle arrest. Antibodies were obtained from the following sources: anti-UGCG (12869-1-AP, Proteintech), anti-SGMS1 (19050-1-AP, Proteintech), anti-SMPD1 (14609-1-AP, Proteintech) and anti-ASAH1 (11274-1-AP, Proteintech); anti-CERS1 (ARP49654_P050, Aviva Systems Biology); anti-GAPDH (60004, Proteintech). anti-mouse secondary antibody (A9044, Sigma-Aldrich), and anti-rabbit secondary antibody (A9169, Sigma-Aldrich).
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