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8 protocols using uk5099

1

Stable Isotope Tracer Metabolomics

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13C3-labeled alanine (CLM-2184-H), 15N-labeled alanine (NLM-454), 13C5-labeled glutamine (CLM-1822-H), 13C3-labeled lactate (CLM-1579), 13C3-labeled pyruvate (CLM-2440), and 13Cx,15Nx-labeled amino acid standard mix (MSK-A2) were acquired from Cambridge Isotope Laboratories. D-glucose (Sigma), DMSO (Sigma), doxycycline hyclate (Sigma), oligomycin (Cayman Chemicals), sodium pyruvate (Sigma), 2-ketobutyric acid sodium salt hydrate (Sigma), rotenone (Cayman Chemicals), FCCP (Cayman Chemicals), antimycin A (Cayman Chemicals), L-alanine (Sigma), L-alanine tert-butyl ester (Alfa Aesar), UK-5099 (Cayman Chemicals), methoxyamine hydrochloride (Sigma), and MTBSTA + 1% TBDMSCl (Sigma).
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2

Authentication and Characterization of Pancreatic Cancer Cell Lines

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MIAPaCa-2, BxPC-3, Capan-1, Panc03.27, Panc10.05, PL45, and HPNE cell lines were obtained from ATCC. PaTu-8902, PaTu-8988T, and YAPC cells lines were obtained from DSMZ. UM6, UM19, UM28, UM32, UM53, and UM76 were generated from primary patient tumors at the University of Michigan. Human pancreatic stellate cells (also described here as hCAFs) were a generous gift from Rosa Hwang (Hwang et al., 2008 (link)). The mCAFs were isolated as described below. All cell lines were cultured in high-glucose DMEM (Gibco) without pyruvate and supplemented with 10% fetal bovine serum (Corning). A 0.25% trypsin (Gibco) was used to detach and passage cells. Cell lines were tested regularly for mycoplasma contamination using MycoAlert (Lonza). All cell lines in this study were validated for authentication using STR profiling via the University of Michigan Advanced Genomics Core. L-Aspartic acid (Sigma), dimethyl-α-kG (Sigma), adenine (Sigma), guanine (Sigma), thymine (Sigma), cytosine (Sigma), sodium pyruvate (Invitrogen), αKB (Sigma), NMN (Sigma), L-alanine (Sigma), and sodium lactate (Sigma) were used at the indicated concentrations. UK5099, AZD3965, and phenformin were purchased from Cayman chemical, Rotenone from Sigma, FX11 from MedChem Express, and IACS-010759 was generously provided by Dr Giulio Draetta, University of Texas MD Anderson Cancer Center.
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3

Quantifying Cell Sensitivity to Pharmacological Agents

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For drug sensitivity assays, cells in the fertile culture were seeded on 12-well dishes at 18,000 cells/cm2 and treated with selected drugs 24hrs later. The arid group was cultured for 0 (acute arid) or 14 (chronic arid) days under arid conditions prior to drug treatment. Cells supplemented daily for 4-5 days with fresh media supplemented with various drugs including: Gemcitabine (Pfizer), PHA-767491 (Cayman chemical), Silvestrol (Biovision), CPI-613 (Cayman chemical), UK 5099 (Cayman chemical) or A-1155463 (Cayman chemical) or vehicle (0.2% DMSO). Tumor cells were fixed at day 0 or endpoint (day 4-5) with paraformaldehyde 4% stained with 3 μM Hoecsht 33342 (Thermo) for 30’ at 37C and quantified using a fluorescence plate reader (Molecular devices) to assess cell numbers. Cell density was normalized for day 0 of each group.
For pharmacological inhibition of biosynthesis under serum repletion, treatment initiated with switch to arid conditions (acute arid) and cells were treated for 72hrs before readouts. Drugs used in that study include: Abemacicilib (MedChem Express), Rapamycin (ApexBio), Torin1 (MedChem Express) and Cycloheximide (Sigma).
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4

Metabolic Compound Screening Protocol

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A detailed list of all compounds included in the metabolic compound screen is available in supplementary Table 1. mTOR inhibitor rapamycin (S1039, Selleckchem), BH3 mimetic ABT-737 (S1002, Selleckchem) and general caspase inhibitor Z-vad-FMK (550,377 BD biosciences) were dissolved in DMSO according to the manufacturer's instructions. Chemicals for the Seahorse experiments oligomycin A (11,342), trifluoromethoxy carbonylcyanide phenylhydrazone (FCCP, 15,218), antimycin A (19,433), rotenone (13,995), UK5099 (16,980), Etomoxir (11,969) and BPTES (19,284) were all purchased from Cayman Chemical (Massachusetts, USA) and dissolved in DMSO according to the manufacturer's instructions. Doxorubicin and cisplatin in a 0.9% NaCl solution were obtained from the in-house hospital pharmacy.
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5

Chemical Reagents for Cell Studies

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DPD (18875), pimozide (16222), LND (14640), and UK-5099 (16980) were purchased from Cayman Chemical. Haloperidol (084-04261), 3,4-dihydroxyphenethylamine hydrochloride, and dopamine hydrochloride (040-15433) were purchased from FUJIFILM Wako Pure Chemical Corporation. Chlorpromazine (C2481) was purchased from Tokyo Chemical Industry Co, Ltd. Y27632 (Y-5301) was purchased from LC Laboratories. (S)-(−)-blebbistatin (B592500) was purchased from Toronto Research Chemicals. For cell culture experiments, all chemical reagents were dissolved in DMSO (FUJIFILM Wako Pure Chemical Corporation) for the stock solution and stored at −20 °C.
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6

Skin Wound Healing in Mice

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All animal experiments were carried out according to our previous WIHN model protocol (1 (link), 26 (link)). In short, 21-day-old male and female mice weighing 8 to 12 g with hairs in the first telogen stage were selected. Mice were anesthetized with isoflurane, shaved, and denuded of 1.44 cm2 full-thickness skin on the lower center of the back, using sterile procedures. The operation day was defined as WD0, and the treatment was performed at WD3 according to each experimental design. At about WD14, the wound scab would fall off. We defined it as scab-detached day (SD0), which is the time point when hair regeneration began. On day 24 after the procedure (WD24), the number of regenerated hair follicles is measured. We visualized the regenerated hair follicles and quantified them using confocal scanning laser microscopy (CLSM), as described before (26 (link)). In GF mice, we performed the procedure in the bubble of the GF laboratory of the Johns Hopkins School of Public Health. In SPF mice, we performed the procedure in a biological safety hood in the Johns Hopkins School of Medicine. S. aureus (1 × 107/50 μl) was injected under the scab on WD3. We also injected 20 μl of 100 nM LW6 (Selleck Chemicals), 1 mM glutamine (Gibco), 200 nM CB839 (Cayman Chemical), 500 nM FX11 (Sigma-Aldrich), or 200 nM UK5099 (Cayman Chemical) under the scab every other day from WD3 to SD0.
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7

Comprehensive Reagents for Cell Metabolism Research

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The chemical and biochemical reagents were obtained from the following sources: ascorbic acid, l-buthionine sulfoximine (BSO), cystine, and L-γ-glutamyl-p-nitroanilide (GPNA) were purchased from Wako Pure Chemicals (Osaka, Japan); oligomycin and 3PO were from Calbiochem-Merck (Darmstadt, Germany); antimycin A1, bis-2-(5-phenylacetamido-1,3,4-thiadiazol-2-yl)ethyl sulfide (BPTES), cilengitide, dimethyl-α-ketoglutarate (DM-αKG), d-glucose, Dulbecco's modified Eagle's medium (DMEM), dimethylsulfoxide, l-glutamine, MEM amino acids solution, MEM non-essential amino acids solution, MEM vitamin solution, N-acetyl-cysteine (NAC), poly 2-hydroxyethyl methacrylate (poly-HEMA), proteinase and phosphatase inhibitor cocktail, sulfasalazine, and 2-deoxy-d-glucose (2DG) were from Sigma-Aldrich (St. Louis, MO, USA); CB839 and UK5099 were from Cayman Chemical (Ann Arbor, MI, USA); etomoxir was from Selleck Chemical (Houston, TX, USA). Antibodies against AMPKα, phosphorylated (p)-AMPKα (Thr172), ASCT2, FAK (Tyr397), p-FAK, IDH1, LKB1, PARP, p-H2AX (Ser139), and xCT were obtained from Cell Signaling (Beverly, MA). Antibodies against GCLC, GCLM, and ME1 were from Abcam (Cambridge, UK). Antibodies against α-tubulin and β-actin were from Wako Pure Chemicals. Antibodies against lamin B1 and Nrf2 were from MBL (Nagoya, Japan) and GeneTex (San Antonio, TX, USA), respectively.
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8

Pancreatic Cancer Cell Line Characterization

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Cell culture: MiaPaCa-2, BxPC-3, Capan-1, Panc03.27, Panc10.05, PL45, and HPNE cell lines were obtained from ATCC. PA-TU8902, PA-TU8988T, and YAPC cells lines were obtained from DSMZ. UM6, UM19, UM28, UM32, UM53, and UM76 were generated from primary patient tumors at the University of Michigan. Human pancreatic stellate cells (hPSCs, also described here as CAFs) were a generous gift from Rosa Hwang 51 (link) . All cell lines were cultured in highglucose Dubelcco's Modified Eagle Medium (DMEM, Gibco) without pyruvate and supplemented with 10% fetal bovine serum (FBS, Corning). 0.25% Trypsin (Gibco) was used to detach and passage cells. Cell lines were tested regularly for mycoplasma contamination using MycoAlert (Lonza). All cell lines in this study were validated for authentication using STR profiling via the University of Michigan Advanced Genomics Core. L-Aspartic acid (Sigma), dimethyl-α-ketoglutarate (Sigma), sodium pyruvate (Invitrogen), α-ketobutyrate (Sigma), nicotinamide mononucleotide (NMN, Sigma), L-alanine (Sigma), and sodium lactate (Sigma) were used at the indicated concentrations. UK5099, AZD3965, and phenformin were purchased from Cayman chemical, rotenone from Sigma, and IACS-010759 was a generous gift from Dr. Haoqiang Ying.
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