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10 protocols using p mtorc1

1

Chondrocyte Apoptosis and Autophagy Regulation

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Eicosapentaenoic Acid (purity, ≥97%), 3-Methyladenine (3-MA, a PI3K inhibitor) and Dorsomorphin (Compound C, an AMPK inhibitor) were purchased from MedChemExpress (NJ, United States). Type II collagenase, TBHP, and dimethylsulfoxide (DMSO) were purchased from Sigma-Aldrich (St Louis, MO, United States). Primary antibodies for cleaved-caspase 3 (C-C3), Beclin-1, LC3B, p-mTORC1, mTORC1, BCL-2, AMPK and p-AMPK were procured from Cell Signaling Technologies (Danvers, MA, United States). Antibodies against BAX, BCL-2, Collagen II, MMP13 and P62 were purchased from Abcam (Cambridge, United Kindom). Antibodies against p-PERK, PERK, p-eIF2α, eIF2α, CHOP, ADAMTS5, Aggrecan, and ATG5 were purchased from ABclonal (WH, CHINA). Antibodies against ATF4, GRP78, Collagen II, and β-actin were purchased from Proteintech (NJ, China). Horseradish peroxidase-labeled secondary antibodies, Alexa Fluor® 488-labeled goat anti-rabbit IgG (H + L) secondary antibody, and Alexa Fluor® 594-labeled goat anti-mouse IgG (H + L) secondary antibody were purchased from Abcam. Further, 4′,6-diamidino-2-phenylindole (DAPI) was purchased from Beyotime (SH, CHINA). The reagents for cell culture were obtained from Gibco (Grand Island, NY, United States).
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2

Angiotensin II-Induced Signaling Pathway

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Ang II was purchased from ENZO (ALX-151-039-M025); collagenase and trypsin were purchased from Gibco (Grand Island, NY, United States); the BCA protein assay kit was bought from Pierce (Rockford, United States); and 2,7-dichlorofluorescindiacetate (DCFH-DA) was obtained from the Bioengineering Institute (Nanjing, China). The following primary antibodies were obtained from Cell Signaling Technology (CST, United States): glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (#2118), p-mTORC1 (#2971), T-mTORC1 (#2983), α-actinin (#69758S), P-p70 S6 kinase (Thr389) (#9234P), T-p70 S6 kinase (#2708), P-JNK (T183/Y185) (#4668P),T-JNK (#9258), P-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) (#4370P), T-ERK (#4695), P-p38 (#4511P), p38 MAPK (#9212P), T-TAK1 (#5206), P-TAK1 (#4508), T-AKT (#4691), P-AKT (#4060), acetyl-CoA carboxylase antibody (#3676), and P-acetyl-CoA carboxylase antibody (#3661S). ABCAM provided the following primary antibodies: Anti-AMPKα2 (ab3760), p-AMPKα2 (S491, ab109402), anti-SOD1 (ab16831), anti-SOD2 (ab38155), Nrf2 (ab15323), 4-hydroxynonenal (ab46545), sarcomeric α-actinin (ab68167), heme oxygenase1 (ab-13243), and NOX2/gp91phox (ab129068). The Sesn2 antibody was acquired from Proteintech (no. 10795-1-AP). Antibodies were used at 1:1,000 dilutions for Western blotting. The secondary antibodies were obtained from LI-COR Biosciences (Lincoln, United States).
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3

Cellular Signaling Pathway Analysis in Frozen Muscle

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Frozen gastrocnemius muscle tissue was ground into small pieces in liquid nitrogen and lysed in a lysis buffer containing cOmplete™ Protease Inhibitor Cocktail and PhosSTOP™ (Roche Diagnostics, Indianapolis, IN, USA), and then centrifuged. A Pierce™ BCA Protein Assay Kit (Thermo Fisher Scientific, Rockford, IL, USA) was used to measure the protein concentration and same concentration of protein of each group was subjected to SDS-PAGE. After transferring, membranes were blocked by 5% skim milk and incubated with a primary antibody overnight. The primary antibodies used for Western blot were p-Akt, Akt, p-mTORc1, mTORc1, p-S6K1, S6K1, p-4E-BP1, 4E-BP1, p-FoxO3a, and FoxO3a (Cell signaling, MA, USA), MuRF1 and Atrogin-1 (Santa Cruz Biotechnology, Santa Cruz, CA, USA), and β-actin (GeneTex, Irvine, CA, USA). The next day, the membranes were incubated with the corresponding secondary antibodies for visualizing the protein bands using LAS3000 luminescent image analyzer (Fuji Film, Tokyo, Japan). β-actin was used as a loading control and Image J software (National Institute of Health, Bethesda, MD, USA) was used for quantification.
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4

Immunoblot Analysis of Signaling Proteins

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U-87, SNB-19 and U-251 cells were lysed in 1% Nonidet P-40 lysis buffer 48 h after transfection with negative control ssRNA, miR-451, or miR-451 inhibitor oligonucleotide. Homogenates were clarified by centrifugation at 20,000 × g for 15 min at 4°C, and protein concentration was measured by the Lowry method. SDS-PAGE gels were loaded with 40 µg of protein from each sample, and resolved proteins were transferred to PVDF membranes (Millipore, Billerica, MA, USA) and incubated with primary antibodies against Rac1 (1:1,000 dilution; Abcam), AMPKα1, p-AMPKα1, mTORC1, p-mTORC1, confilin or p-confilin (1:1,000 dilution; Cell Signaling Technology, Danvers, MA, USA), followed by incubation with an HRP-conjugated secondary antibody (1:1,000 dilution; Zymed, San Diego, CA). The specific protein was detected using the SuperSignal protein detection kit (Pierce, Waltham, MA, USA). After washing with stripping buffer, the membrane was reprobed with antibody against GAPDH (1:1000 dilution; Santa Cruz Biotechnology, Santa Cruz, CA, USA).
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5

Antibody Panel for Cellular Signaling

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The following antibodies were used for IHC and Western immunoblotting: ATF4 (catalog 10835-1-AP) and SKP2 (catalog 15010-1-AP) from Proteintech; CHOP (catalog 2895), p-YAP (catalog 13008, S127), YAP (catalog 14074), p27 (catalog 3686), MYC (catalog 9402), p-RPS6 (catalog 4858, S235/236), t-RPS6 (catalog 2217), p-mTORC1 (catalog 5536, S2448), t-mTORC1 (catalog 2983), p-ERK1/2 (catalog 9101, T202/Y204), t-eIF2α (catalog 2103), p-AKT (catalog 9271, S473), t-AKT (catalog 4691), EIF4FBP1 (catalog 2855, T37/46), K48-Ub (catalog 8081), p-PERK (catalog 3179, T980), and PERK (catalog 3192) from Cell Signaling Technology; CYR61 (catalog E-AB-14920), CTGF (E-AB-12339), and aquaporin 2 (E-AB-30540) from Elabscience Biotechnology; CDK1 (catalog SC-54) and t-ERK1/2 (catalog SC-94) from Santa Cruz Biotechnology; α-tubulin (catalog T5168) and K63-Ub (catalog 05-1308) from MilliporeSigma; PCNA (catalog MS-106-P1ABX and, p-LATS1/2 (catalog PA5-64591, S809/S872) from Thermo Fisher Scientific; Oct4 (catalog NB100-2379) from Novus Biologicals; Sox2 (catalog ab97959), vimentin (catalog ab92547), Ki-67 (clone SP6), p-eIF2α (catalog ab32157, S51), BIM (catalog ab32158), and TAZ (catalog ab224239) from Abcam; GRP78 (catalog A0241) from StressMarq Biosciences; and nestin 1 (monoclonal rat-401s) from DSHBU Iowa.
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6

Molecular Signaling Pathway Analysis

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Primary antibodies against Bcl-2, Bax, Bad, and Bcl-xL were procured from Abcam (USA). Akt, p-Akt, mTORC1, p-mTORC1, mTORC2, p-mTORC2, phosphatase and tensin homolog (PTEN), glycogen synthase kinase 3β (GSK-3β), p- GSK-3β (Ser9), NF-κBp65, and cleaved caspase-3 were procured from Cell Signaling Technology (Danvers, MA, USA). CyclinD1, β-actin, and horseradish- and peroxidase-labeled IgG secondary antibodies were purchased from Santa Cruz Biotechnology (Dallas, TX, USA) and used for expression analysis. Cell lysis buffer for Western blotting analysis was purchased from Beyotime Institute of Biotechnology (Beijing, China). Mangiferin and isoflurane were procured from Sigma-Aldrich (St. Louis, MO, USA). All other chemicals used for analysis were obtained from Sigma-Aldrich.
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7

Metabolic Regulation in Cell Lines

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Ritonavir was purchased from Euroasia Inc., and metformin, dimethyl α-ketoglutarate (DMK) and 6-Diazo-5-oxo-L-norleucine from Sigma-Aldrich. The following antibodies were purchased: MCL-1 (Santa Cruz Biotechnology) and GAPDH from Millipore; pAKT (S473), AKT, pAMPK (T172), AMPK, mTORC1, and pmTORC1 from Cell Signaling Technology. Antisera to human GLUT4 was generously provided by Dr. S. Cushman (National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD). Oligomycin, carbonyl cyanide p-trifluoro-methoxyphenyl hydrazone, antimycin, and rotenone were purchased from Sigma.
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8

PTZ-Induced Signaling Pathway Analysis

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PTZ (P6500) (Sigma-Aldrich, St. Louis, MO, USA) was dissolved in freshly prepared saline solution prior to administration. Antibodies against Akt, p-Akt, GSK-3β, mTORc1, p-mTORc1, mTORc2, p-mTORc2, cleaved caspase-3, BDNF, TrkB and nGAD65 were purchased from Cell Signaling Technology (Danvers, MA, USA). GABAA, p-GSK-3β, Phosphatase and tensin homolog (PTEN), Bax, Bcl-2, Bad, Bcl-xL and β-actin were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA) and were used for expression analysis. Nobiletin and the remaining chemicals were obtained from Sigma-Aldrich.
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9

Antibodies and Reagents for Cellular Signaling

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Antibodies against P-Akt (#4060), P-mTORC1 (#5536), P-S6K (# 9234), P-PLCγ2 (#3871), and β-actin (#4967) were from Cell Signaling (Beverly, MA, USA); a pan histone antibody was from Sigma (#MABE71). Ficoll-Paque Plus was from GE Biosciences (Baie d’Urfé, Qc, Canada); Dextran T500 from Pharmacosmos (Holbæk, Denmark); endotoxin-free (< 2 pg/ml) RPMI 1640 from Wisent (St-Bruno, Qc, Canada); poly-L-lysine from Peptides International (Louisville, KY, USA). Recombinant human cytokines were from R&D Systems (Minneapolis, MN, USA. Dimethyl sulfoxide (DMSO), N-formyl-methionyl-phenylalanine (fMLF), and phenylmethanesulphonyl fluoride (PMSF) were from Sigma-Aldrich (St. Louis, MO, USA). All inhibitors were purchased through Cedarlane Labs (Missisauga, Canada). ProLong Gold Antifade, Hoechst 33342, propidium iodide, and 16% paraformaldehyde (PFA) were purchased from Thermo Fisher (Missisauga, Canada). PlaNET reagents (fluorescent chromatin-binding polymers) are no longer available from Immune Biosolutions or other suppliers; we therefore employed a close equivalent – fluorescent, 50-nm carboxylate microspheres (# 16661-10) from Polysciences Inc. (Warrington, PA, USA). These microspheres are referred to as PlaNET reagents throughout this study. All other reagents were of the highest available grade, and all buffers and solutions were prepared using pyrogen-free clinical grade water.
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10

Panobinostat and Sodium Butyrate Induce Apoptosis in CML Cell Lines

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Human CML cell line K562 was obtained from the American Type Culture Collection (ATCC, Rockville, MD). K562/ADR, an adriamycin–resistant cell line, and K562/G, an imatinib–resistant cell line, were kindly provided by Dr. Wei He (Institute of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, China). All cells were maintained in RPMI‐1640 medium (Hyclone Laboratories) supplemented with 10% defined FBS (Hyclone Laboratories). Cells were cultured at 37°C in 5% CO2. Panobinostat (LBH589) was purchased from Selleck Chemicals (Houston, TX). Sodium butyrate (NaBu) was purchased from Sigma‐Aldrich (St. Louis, MO). The primary antibodies against β‐ACTIN, GAPDH, caspase‐3, caspase‐6, caspase‐8, caspase‐9, PARP, BIP, BCL‐XL, MCL‐1, BAX, BAK, BAD, XIAP, survivin, ABCG2, MDR1, BCR/ABL, p‐BCR/ABL, AKT, p‐AKT, mTOR, p‐mTORC1, 4EBP1, p‐4EBP1, eIF4E, p‐eIF4E and c‐MYC were purchased from Cell Signaling Technology (Danvers, MA), the antibody against caspase‐7 was purchased from Abcam (Cambridge, UK).
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