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15 protocols using everolimus

1

Pilocarpine-induced Seizure Model in Mice

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Two- to three-month-old male35 (link) littermates (WT, Pik3c2b HET and Pik3c2b KO) were put into separate cages and injected intraperitoneally with 1 mg/ml atropine sulphate (Sigma Aldrich, #A0257) dissolved in PBS.36 After 30 min, mice were injected intraperitoneally with 350 mg/kg pilocarpine hydrochloride (Sigma Aldrich, #P6503) and scored for seizures for 90 min. For everolimus rescue experiments, mice were injected intraperitoneally with 10 mg/ml everolimus (Cayman Chemical, #11597) dissolved in PBS 5% Tween-20 60 min before atropine injection. Mice behaviours were scored on a scale ranging from 1 to 7 (1 = immobility; 2 = tail extension; 3 = repetitive movements; 4 = forelimb clonus, rearing and falling; 5 = repetitive stage 4; 6 = epileptic seizure; 7 = death).37 (link) Observers were blinded to the genotype of animals.
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2

Cell Line Cultivation and Authentication

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MHCC-97H and HCC-LM3 cells were purchased from the Liver Cancer Institute of Fudan University, Shanghai, China. Huh7, Hep3B and HepG2 cells were purchased from the China Center for Type Culture Collection (CCTCC, Wuhan, China). The cells were cultured in Dulbecco’s modified Eagle’s medium (Invitrogen Corporation, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (Life Technologies Inc., Gibco/Brl Division, Grand Island, NY, USA) in a humidified atmosphere comprising 5% CO2 at 37 °C. The HepG2 and Hep3B cell lines were authenticated by comparative genomic array hybridization or short tandem repeat DNA profiling according to the ATCC database, which was performed within less than 10 passages after authentication and less than 20 passages after receipt from commercial suppliers. The other cell lines were identified using the STR genotyping test method by Wuhan Genecreate Biological engineering Co., Ltd., China.
Puromycin, everolimus, rapamycin and LY364947 (a TβR1 inhibitor) were purchased from Cayman Chemical Company (Ann Arbor, MI, USA).
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3

Glioma Tumorsphere Culture and Chemotherapeutic Testing

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This study was conducted in accordance with Declaration of Helsinki. All tumor and blood samples were collected with patient consent under protocols approved at Yokohama City University (YCU) Hospital and Massachusetts General Hospital (MGH) Institutional Review Boards. To create glioma tumorsphere lines, fresh tumor specimens were obtained from surgery and enzymatically dissociated with 0.1% of Trypsin and DNase. Tumorsphere lines were cultured in serum-free neural stem cell medium, as previously described (3 (link),25 (link),28 (link)). All tumorsphere lines were cryopreserved less than passage 3 to use for in vitro experiments. Temozolomide (TMZ, Sigma), Nimustine (ACNU, Tokyo Chemical Industry), Lomustine (CCNU), Procarbazine (Sigma), Vincristine (Sigma), FK866 (Sigma), LY294002 (Sellek), GDC-0068 (Cayman), BYL719 (Cayman), Everolimus (Cayman), and AGI-5198 (Sigma) were used.
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4

Evaluating SMI-Induced Cytotoxicity in MCF-7 Cells

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Three SMIs, including everolimus (mTOR inhibitor), MK-2206 (AKT inhibitor), and ibrutinib (BTK inhibitor), were applied in this study (Cayman, USA). These chemical reagents were dissolved in dimethyl sulfoxide (DMSO) (Merck, Germany), and aliquots were frozen. The MCF-7 cells were seeded in 96-well culture plates (SPL, South Korea) in a 200 μL fully supplemented medium in the presence of various drugs at concentrations ranging from 16 to 8192 nM and incubated for 48 hours to determine the half-maximal inhibitory concentration (IC50) values for all SMIs. Subsequently, each well was filled with 20 μL of freshly prepared 5 mg/mL of MTT solution (Sigma-Aldrich, USA) and incubated at 37 °C for 4 hours. Following incubation, the medium was carefully removed, and the reduced formazan crystals were dissolved in 150 μL DMSO by incubating at 37°C for 30 minutes in the dark. Optical density (OD) values were measured at 570 and 630 nm using an enzyme-linked immunosorbent assay plate reader (Synergy H1 BioTek, USA). All the experiments were performed in triplicates. The relative cell proliferation was calculated by dividing the mean OD values of each group by the OD values obtained from the control group.
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5

Cell Line Maintenance and Drug Treatment

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The human PC cell lines Capan1 (HBT-79), MiaPaca2 (CRL-1420), Panc1 (CRL-1469) and Cos7 (CRL-1651) cell lines were purchased from American Tissue Cell Culture (Manassas, Virginia, USA) and maintained under culture with DMEM (Gibco) High Glucose containing 2 mM glutamine (Invitrogen), 5000 U/mL Penicillin-Streptomycin (Gibco) and 10% heat-inactivated dialyzed fetal bovine serum (Invitrogen). For drug treatment, Everolimus (11597, Cayman Chemical), CB-839 (22038, Cayman Chemical) or BPTES (S7753, Aurogene) were added the day after seeding in culture media. Cells were counted at the indicated time point with CellTiter-Fluor Cell Viability Assay (Promega). Human cell lines authentication was performed by BMR Genomics. All cell lines were routinely tested for Mycoplasma contamination using PCR.
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6

Comprehensive Compound Screening Library

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The following compounds were used in the present study: etoposide (Sigma-Aldrich, E1383), 4-hydroxytamoxifen (Sigma-Aldrich, H7904), ouabain (Apexbio, B2270), navitoclax (Apexbio, A3007), ginkgetin (Cayman Chemical, 25103-1 mg), oleandrin (Cayman Chemical, 29871-1 mg), periplocin (Cayman Chemical, 25216-1 mg), BMS 599626 dihydrochloride (Apexbio B5792), BMS 986142 (BioVision, B2420-1), ellagic acid (Apexbio, A2306), everolimus (Cayman Chemical, 22559-1 mg), herbacetin (Cayman Chemical 19285-1 mg), morin (MedChemExpress LLC, HY-N0621-10mg), paritaprevir (MedChemExpress HY-12594), rapamycin (Cayman Chemical, 13346-5 mg), taurocholic acid sodium salt hydrate (Selleck Chemicals, S5130), velpatasvir (BioVision, B1194-5), verteporfin (Apexbio, A8327), zotarolimus (Cayman Chemical, 29246-5 mg), gamma mangostin (MedChemExpress LLC, HY-N1957-5mg), gamma oryzanol (MedChemExpress LLC, HY-B2194), gossypol (MedChemExpress LLC, HY-15464A-10mg), ridaforolimus (Apexbio, B1639), scutellarein (MedChemExpress LLC, HY-N4314-1mg), vinblastine sulfate (MP Biomedicals LLC, 0219028725).
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7

Affinity-based Protein Purification Reagents

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MG132 (S2619), BI-D1870 (S2843), and cycloheximide (S6611) were purchased from Selleck. Puromycin (P8833), Blasticidin (15205), iodonitrotetrazolium chloride (I10406), MTT (475989), anti-Flag agarose beads (A-2220), anti-HA agarose beads (A-2095), and glutathione agarose beads (G4510) were purchased from Sigma-Aldrich. Rapamycin (13346), Torin2 (14185), MK2206 (11593), GSK2110 (17988), S6K1-I (15018), Pazopanib (12097), Crizotinib (12087), Everolimus (11597), and Temsirolimus (11590) were purchased from Cayman Chemical. Active RSK3 protein (50-199-8827) was purchased from Thermo Fisher Scientific. JR-AB2-011 (HY-122022) was purchased from MedChemExpress.
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8

Autophagy Flux Monitoring Workflow

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Autophagy flux reporter cells were generated via retroviral transduction of U87.CD4.CCR5 cells (obtained via the NIH AIDS Reagent Program, Division of AIDS, NIAID, NIH) cells with pBABE-mCherry-GFP-LC3 (Addgene 22418) as described previously100 (link) referred to herein as U87.LC3-mCherry-GFP cells. Cells were maintained in Iscoves Modified Dulbecco’s Medium (IMDM, Thermo Fisher Scientific) supplemented with 10% FBS and 1% penicillin/streptomycin. To confirm autophagy-flux-enhancing potential of therapeutics, U87.LC3-mCherry-GFP cells were treated for 24 h with 100 uM carbamazepine (Tocris), 3 nM everolimus, or 5 uM MK-2206 (both Cayman Chemical) after which GFP reduction was determined on a Fortessa Cell Analyzer.
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9

Antibody Characterization for Co-IP and Western Blot

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For Co-IP and western blots, the following antibodies were obtained commercially: mouse anti-Flag (M2, F1804), mouse anti-vinculin (V9131), and mouse anti-tubulin (T5168) (Sigma, St. Louis, MO); rabbit anti-WDR5 (#13105), rabbit anti-RBBP5 (#13171), rabbit anti-KMT2A/MLL1-C (#14197), rabbit anti-CXXC1(#12585), rabbit anti-HCFC1 (#69690), rabbit anti-WDR82 (#99715), rabbit anti-phospho p70 S6K (Thr389) (#9205), rabbit anti-p70 S6K (#9202), rabbit anti-phospho 4E-BP1 (Thr37/46) (#2855), rabbit anti-4E-BP1 (#9644), and anti-cleaved caspase 3 (#9661) (Cell Signaling Technology, Danvers, MA, USA); rabbit anti-DPY30 (A304-96A) (Bethyl Laboratories, Montgomery, TX, USA).
For drug treatment experiments, WDR5 inhibitor OICR-9429 (Sigma, SML1209 and Cayman Chemical, #16095) and control OICR-0547 (Structural Genomics Consortium), and mTOR inhibitors, OSI-027 (Cayman Chemical, #17379), everolimus (Cayman Chemical, #11597), and temsirolimus (Cayman Chemical, #11590) were used. Compounds of WDR5 degrader MS67 and negative control MS67N were synthesized in Jian Jin’s lab.
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10

Pharmacological Agents in Research

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Sources of pharmacological agents were as follows: WST‐1 (Dojindo, Kumamoto, Japan), T16inh‐A01 (Tocris Bioscience, Bristol, UK), everolimus (Cayman Chemical, Ann Arbor, MI, USA), AZD 5363 (Cayman Chemical), MHY 1485 (Cayman Chemical), and DPP (Cayman Chemical). Other agents were obtained from Sigma‐Aldrich (St Louis, MO, USA) or Wako Pure Chemical Industries (Osaka, Japan).
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