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9 protocols using 3 methyladenine m9281

1

Endothelial Cell Culture and Pharmacological Treatments

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C57BL/6 mouse primary brain microvascular endothelial cells isolated from brain tissue of P2 pups were purchased from Cell Biologics (Chicago, IL, USA). Cells were cultured at 37 °C, in a humidified environment, in the presence of 5% CO2. They were fed every 2 days with a complete mouse endothelial cell culture medium, on 60 mm diameter dishes or 12-well slides. Two days after confluence was reached, the cells were incubated for 24 h with serum-free medium. The cells were then treated with various pharmacological agents, including 50 mM ethanol, 100 μM acetaldehyde, lysosomal protease inhibitors 10 μg/ml pepstatin A (P-5318, Sigma-Aldrich, St Louis, MO, USA) and 10 μg/ml E64D (sc-201280 A, Santa Cruz Biotechnology), 200 nM rapamycin (R0395, Sigma-Aldrich), 100 nM Bafilomycin A1 (B-1793, Sigma-Aldrich), 10 mM 4-methylpyrazole (4-MP, M-1387, Sigma-Aldrich), 30 mM 3-methyladenine (M9281, Sigma-Aldrich), 75 nM wortmannin (W3144, Sigma-Aldrich), Krebs medium (145 mM NaCl, 4.75 mM KCl, 1.18 mM KH2PO4, 1.18 mM MgSO4 hydrate, 25 mM NaHCO3, 2.5 mM CaCl2, pH 7.4) – this medium is commonly used for starvation condition, and ethanol (25 to 200 mM).
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2

Molecular Mechanisms of Mitophagy Regulation

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The immortalized RPTC cell line was originally obtained from Dr. Ulrich Hopfer (Case Western Reserve University) and maintained in DMEM/F-12 medium supplemented with 10% fetal bovine serum and growth factors [47]. The retrovirus packaging cell line (293-Phoenix) was provided by Drs. Xiongjie Jin and Nahid F. Mivechi (Augusta University). The cells were cultured in DMEM medium with 10% fetal bovine serum. Primary antibodies: anti-LC3B (NB100-2220), anti-PINK1 (BC100-494) and anti-FUNDC1 (NBP1-81063) were from Novus Biologicals; anti-SQSTM1 (ab56416), anti-IMMT/MIC60 (ab110329), anti-COX4I1 (ab153709) and anti-PPIB (ab16045) were from Abcam; anti-TOMM20 (sc-11415), anti-PINK1 (sc-517353), anti-PRKN (sc-133167), anti-BNIP3L/NIX (sc-166332) and anti-HSPD1 (sc-13966) were from Santa Cruz Biotechnology; anti-CASP3 (9665) and anti-cleaved CASP3 (9664) were from Cell Signaling Technology; anti DNM1L (BD Biosciences, 611113); anti-ACTB (Sigma-Aldrich, A5316). Secondary antibodies for immunoblot analysis were from Jackson ImmunoResearch Laboratories. CCCP (C2759), chloroquine (C6628) and 3-methyladenine (M9281) were from Sigma-Aldrich. BECN1 peptide (Tat-BECN1, sequence: YGRKKRRQRRRGGTNVFNATFEIWHDGEFGT) and its control peptide (Tat-scrambled, sequence: YGRKKRRQRRRGGVGNDFFINHETTGFATEW) were synthesized by GenScript.
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3

Aurantiamide Acetate Modulates Autophagy

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Aurantiamide acetate was isolated from the aerial parts of C. terniflora DC in our laboratory. Cisplatin was provided by QiLu Pharmaceutical (Jinan, China). Bafilomycin A1 (BafA1; BML-CM110-0100) and rapamycin (BML-A275-0005) were obtained from Alexis Biochemicals (Lausen, Switzerland). 3-methyladenine (M9281) and chloroquine (CQ; C6628) were bought from Sigma-Aldrich (Shanghai) Trading Co., Ltd, Shanghai, China. EYFP (enhanced yellow fluorescence protein)-Golgi plasmid was purchased from Clontech Laboratories, Inc., Mountain View, CA, USA. MitoTracker Red CMXRos and propidium iodide (PI) were from Invitrogen Life Technologies, CA, USA Carlsbad. Alexa Fluor 488 Phalloidin was obtained from Molecular Probes, Inc., Eugene, OR, USA. DMEM and heat-inactivated horse serum were obtained from GIBCO-BRL, New York, NY, USA. Foetal calf serum (FCS) was purchased from Hangzhou Tianhang Biological Technology Co., Ltd., Hangzhou, China. Anti-LC3 and anti-actin primary antibody was purchased from Cell Signaling Technology Shanghai Biological Reagents Co., Ltd., Shanghai, China, and Santa Cruz Biotechnology (Shanghai) Co., Ltd., China respectively.
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4

Colon Cancer Cell Line Maintenance

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Human colon cell lines (HT-29, SW480, SW620, HCT116, and HRT18) were purchased from the American Type Culture Collection (ATCC) in 2010, maintained in our laboratory, and cultured with RPMI-1640 medium supplemented with 10% fetal bovine serum (Life Technologies) at 37 °C in 5% CO2. The cell lines were routinely tested for presence of mycoplasma with 4,6-diamidino-2-phenylindole staining, and were mycoplasma free.
Antibodies and reagents. Antibodies against RACK1 (sc-17754), Cyclin D1 (sc-450), Bax (sc-20067), cleaved PARP (sc-56196), Bcl-2 (sc-509) and JNK-2 (sc-7345) were purchased from Santa Cruz. Antibodies against SQSTM1 (ab207305), BECN1 (ab62557) and LC3-II (ab192890) were purchased from Abcam. Antibodies against LC3-I/II antibody (#4108) and phospho-JNK-1/2(#9255) were purchased from CST. Horseradish peroxidase-conjugated goat anti-rabbit (#A24531) and anti-mouse IgG antibodies (#A24512) were purchased from Life Technologies. Bafilomycin A1 (B1793) and 3-methyladenine (M9281) were purchased from Sigma-Aldrich.
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5

Autophagy and Cell Death Regulation

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Anti-SIRT1 antibody (ab104833), anti-LC3 antibody (ab63817), and anti-acetyl lysine antibody (ab80178) were purchased from Abcam (Abcam Shanghai office launch, Shanghai, China). Sevoflurane (H20070172) was from the Shanghai Henrui Biomedical Company (Shanghai, China). A cell death-detecting kit (11684817910) was from Roche (Indianapolis, Indiana, USA). 3-methyladenine (M9281) and nicotinamide (N0636) was from Sigma (St. Louis, MO, USA).
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6

Modulation of BPDE and CSE-induced Cellular Responses

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Synthesized benzo[a]pyrene diol epoxide (BPDE) was kindly provided by Dr. Shantu Amin (Department of Pharmacology, Penn State College of Medicine, Hershey, PA) [17 (link)] and dissolved in anhydrous dimethyl sulfoxide. CSE was prepared as described previously [18 (link)] and expressed as total particulate material (μg/mL) for treating cells. Chloroquine diphosphate salt (Cat. No. C6628), wortmannin (W1628), and 3-methyladenine (M9281) were obtained from Sigma (St. Louis, MO). Recombinant human transform growth factor-β (TGF-β) was purchased from eBioscience (San Diego, CA). Primary Antibodies used were anti-vasorin/vasorin (MAB2140; R&D Systems, Minneapolis, MN), ATG-7 (PA5-17216; Thermo Fisher Scientific, Grand Island, NY), β-actin (A2103; Sigma), β-tubulin (T8328; Sigma), LC3B (L7543; Sigma), p62 (610833; BD Biosciences, San Jose, CA), PARP1 (BML-SA248; Enzo Life Sciences, Farmingdale, NY), phospho-Smad2 (3101; Cell Signaling, Danvers, MA), Smad2 (3103; Cell Signaling), and GAPDH (sc-32233; Santa Cruz Technologies, Santa Cruz, CA).
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7

Doxorubicin-Induced Autophagy Signaling

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Doxorubicin (c-200,923) was purchased from Santa Cruz Biotechnology. 3-methyladenine (M9281) was purchased from Sigma-Aldrich. Primary antibodies against histone H3 (4499), lamin A/C (4777), SQSTM1/P62 (5114), SUMO-1 (4930) and p-histone H2A.X (Ser139, 9718) were purchased from Cell Signaling Technology. GAPDH (sc-25,778) and UBC9 (sc-10,759) were purchased from Santa Cruz Biotechnology. LC3B (L7543) was purchased from Sigma Aldrich. Peroxidase-labeled antibody to mouse IgG (074–1802) and peroxidase-labeled antibody to rabbit IgG (074–1516) were purchased from Kirkegaard and Perry Laboratories. Alexa Fluor 488 goat anti-rabbit (A21206) and Alexa Fluor 647 donkey anti-mouse (A21235) were purchased from Molecular Probes.
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8

Autophagy regulation by pharmacological agents

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VES (T3126), chloroquine (C6628), 3-methyladenine (M9281) and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) (88417) were purchased from Sigma. Primary antibodies used for western blotting were rabbit anti-LC3 (Sigma, L7543), rabbit anti-Akt (Cell Signaling, 9272), rabbit anti-p-Akt (S473) (Cell Signaling, 9271S), rabbit anti-mTOR (Cell Signaling, 2972S), rabbit anti-p-mTOR (Ser2448) (Cell Signaling,5536S), rabbit anti-p70S6K (Cell Signaling,5707S), rabbit anti-p-p70S6K (T389) (Cell Signaling, 9205S), rabbit anti-4E-BP-1(Cell Signaling, 8594S), rabbit anti-p-4E-BP-1 (Thr37/46) (Cell Signaling, 9459S), rabbit antip38 MAPK (Cell Signaling,,8690S), rabbit anti-p-p38 MAPK (The180/Tyr1820) (Cell Signaling, 4092), rabbit anti-5'Adenosine monophosphate-activated protein kinase α (AMPKα) (Cell Signaling, 5831S), rabbit anti-p-AMPKα (Thr172) (Cell Signaling, 2535S) and rabbit anti-Actin (Santa Cruz Biotechnology, sc-1616). Alkaline phosphatase conjugated second antibody used for western blotting was anti-rabbit IgG (promega, S373B). Green fluorescent protein—microtubule associated protein 1 light chain 3 (GFP-LC3) plasmid was obtained from YRGene, China (Yrbio, VXY0542). All cell culture solutions were obtained from Thermo and all plastic-ware was obtained from Nunc, unless otherwise stated.
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9

Hepatocellular Carcinoma Cell Line Cultivation and Compound Preparation

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Human HCC cell lines, HepG2 (TP53wt) (ACC-180) and Hep3B (TP53null) (ACC-93) (DSMZ, Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig Germany) were cultured under standard conditions as previously described [18 (link)]. Panobinostat was kindly provided by Novartis Pharma AG (Basel, Switzerland) and prepared as previously described [18 (link)]. 4-Hydroxytamoxifen was a kind gift from Heidi Griesmann (Department of Gastroenterology and Endocrinology, Philipps University of Marburg). 3-methyladenine (M9281) and Bafilomycin (B1793) were purchased from Sigma-Aldrich.
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