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11 protocols using pyrazofurin

1

Cell Growth, Colony Formation, and Pyrazofurin Effect

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For the cell growth curve, 2500 cells were plated in one well of a 96‐well plate with at least three repeats for each cell, and Cell Counting Kit‐8 (CCK‐8, Dojindo, Tokyo, Japan) was used to perform continuous detection for 4–5 d. For the colony formation assay, 1000 cells were plated in one well of a 6‐well plate with at least three repeats for each cell and, 7–9 d later, were stained with crystal violet. Image J was used for colony number counting. To assay the effect of pyrazofurin (Sigma‐Aldrich, St. Louis, USA, #SML1502) on cell growth, 1500 cells were plated in one well of a 96‐well plate with at least three repeats for each condition, and the next day, pyrazofurin or vehicle was added. CCK‐8 was used to perform the continuous detection for 4–5 d.
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2

Small Molecule Compound Preparation and Storage

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Erastin2 and ML162 were synthesized at Acme Bioscience. Nutlin-3 (Cat. no. S1061), nutlin-3b (Cat. no. S8065), gemcitabine HCL (Cat. no. S1149), and MI-773 (Cat. no. S7649) were purchased from Selleck Chemicals. Pyrazofurin (Cat. no. SML1502), HU (Cat. no. H8627), MPA (Cat. no. M5255), ferrostatin-1 (Cat. no. SML0583), Doxycycline hyclate (Cat. no. D9891), and L-BSO (Cat. no. B2515) were purchased from Sigma-Aldrich. BSO and gemcitabine HCL were dissolved directly into cell media. C11-BODIPY 581/591 was prepared as a stock solution in methanol and stored before use at −20°C. All other compounds were prepared as stock solutions in DMSO and stored before use at −20°C.
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3

Synthesis of (R)-2-Hydroxyglutarate Ester

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TFMB ester of (R)-2-hydroxyglutarate was generated as previously described by R. Looper at University of Utah (Losman et al., 2013 (link)). BAY 2402234 was provided by Bayer Pharmaceuticals. Where indicated, cell culture media also contained the following additives: brequinar (Sigma-Aldrich), 6-azauridine (Sigma-Aldrich), pyrazofurin (Sigma-Aldrich), uridine (Sigma-Aldrich), lometrexol (Cayman), AGI-5198 (XcessBio), deoxythymidine (Sigma-Aldrich), deoxycytidine (Sigma-Aldrich), palbociclib (Cayman), tunicamycin (Sigma-Aldrich).
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4

Evaluating Anti-SARS-CoV-2 Agents in vitro

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MRC-5 cells and the HCoV-229E strain were purchased from the American Type Culture Collection (ATCC; Manassas, VA, USA). All media ingredients and the XTT-based viability assay kit were purchased from Biological Industries (Beit HaEmek, Israel). Cannabidiol (CBD) was purchased from Recipharm Israel (Ness Ziona, Israel). NT-VRL-1 formulation was obtained from Eybna Technologies (Givat Hen, Israel). Glycyrrhizin was obtained from Penta International Corporation (New Jersey, NJ, USA) and pyrazofurin was purchased from Sigma (Jerusalem, Israel).
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5

Purine Metabolism Regulation Protocol

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Thymidine, hypoxanthine, sodium formate, adenine, adenosine, guanosine, deoxyuridine, H2O2 and pyrazofurin are from Sigma Aldrich. AICAr is from Chemtronica. Febuxostat is from Stratech Scientific Ltd. Allopurinol and Uric acid were from Merck Life Science UK.
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6

High-Throughput Cell Viability Screening

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Drugs were spotted using a Tecan D300e dispenser (Tecan, Mannedorf, Switzerland) at the following concentrations with log2 dilution series. pyrazofurin (SML1502, Sigma-Aldrich) (200 μM–5 μM for U2OS and hTERT-RPE1; 200 μM–2 μM for MCF7), MPA (M5255, Sigma-Aldrich) (100 μM–0.05 μM), 6MP (38171, Merck) (100 μM–0.05 μM), glutamine starvation (2 mM-7.8 μM), brequinar (5.08321 Sigma-Aldrich) (200 μM–10 μM), and leflunomide (L5025, Sigma-Aldrich) (400 μM–10 μM), hydoxyurea (H8627, Sigma-Aldrich) (5 mM–0.05 mM). Five hundred cells per well were seeded on 384-well cell culture plates, and viability was assessed with a resazurin assay and read on a Hidex Sense or Molecular Devices ID5 plate reader after 4 days in technical triplicates. Uridine (U3750, Sigma-Aldrich) rescue was performed at a concentration of 500 μM for 24 h. 2-DG (10 mM) was added to cultured cells for 48 h. Doxorubicine (D1515, Sigma-Aldrich), actinomycin D (A1410, Sigma-Aldrich), olaparib (AZD2281, Selleckchem), camptothecin (C9911, Sigma-Aldrich), nutlin3a (SML0580, Sigma-Aldrich).
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7

Antiviral Evaluation of Phytochemicals

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MRC-5 cells, HCoV-229E strain HCoV-OC43, and influenza A (H1N1) virus were purchased from the American Type Culture Collection (ATCC; Manassas, VA). All media ingredients and cell-proliferation kits (XTT) were purchased from Biological Industries (Israel). CBD was purchased from Recipharm Israel Ltd. (Israel). NT-VRL®ฏ was obtained from Eybna Technologies Ltd. (Israel). Glycyrrhizin was obtained from Penta International Corporation (NJ, USA) and pyrazofurin was purchased from Sigma Corporation (Israel). Commercial frozen human peripheral blood mononuclear cells (PBMCs) for the cytotoxicity and cytokine secretion assays were purchased from Lonza (Switzerland).
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8

Comprehensive Chemical Compound Library

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A library of 262 board-spectrum chemical compounds was kept in 96-well plate format with a concentration of 10 ​mmol/L. The list of compounds is provided in Supplementary Table S1. Vidofludimus (Selleck, USA, S7262) was dissolved in dimethyl sulfoxide (DMSO) with a stock concentration of 10 ​mmol/L. Pyrazofurin (Sigma-Aldrich, USA, SML1502) was dissolved in H2O with a stock concentration of 10 ​mmol/L. Uridine (Merck, USA, U3750) was dissolved in H2O with a stock concentration of 10 ​mmol/L. Ribavirin (Merck, USA, R9644) was dissolved in DMSO with a stock concentration of 10 ​mmol/L. Human interferon Alpha 2A (PBL assay science, USA, 11100-1) was dissolved in phosphate buffered saline (PBS) supplemented with 0.1% bovine serum albumin (BSA). HEV ORF2 polyclonal antibody was kept in our laboratory. Anti-rabbit, anti-mouse peroxidase-conjugated and anti-rabbit 594-conjugated secondary antibodies were purchased from Jackson ImmunoResearch (USA). GAPDH antibody (60004-1-lg) was obtained from Proteintech (China).
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9

Synthesis of (R)-2-Hydroxyglutarate Ester

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TFMB ester of (R)-2-hydroxyglutarate was generated as previously described by R. Looper at University of Utah (Losman et al., 2013 (link)). BAY 2402234 was provided by Bayer Pharmaceuticals. Where indicated, cell culture media also contained the following additives: brequinar (Sigma-Aldrich), 6-azauridine (Sigma-Aldrich), pyrazofurin (Sigma-Aldrich), uridine (Sigma-Aldrich), lometrexol (Cayman), AGI-5198 (XcessBio), deoxythymidine (Sigma-Aldrich), deoxycytidine (Sigma-Aldrich), palbociclib (Cayman), tunicamycin (Sigma-Aldrich).
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10

Comprehensive Cell Growth Analyses

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For cell growth curve, 1500 cells were plated in one well of 96-well plate with at least 3 repeats for each cell and Cell Counting Kit-8 (CCK-8, Dojindo, Tokyo, Japan) was used to do continuous detection for 4–5 days. For colony formation assay, 1000 cells were plated in one well of 6-well plate with at least 3 repeats for each cell and 7–9 days later were stained with crystal violet. Image J was used for colony number counting. For pyrazofurin (SML1502, Sigma-Aldrich, St. Louis, USA) affecting cell growth, 1500 cells were plated in one well of 96-well plate, with at least 3 repeats for each condition and the next day pyrazofurin or vehicle was added. CCK-8 was used to do the continuous detection for 4–5 days. For cell cycle, one million of cells were harvested and fixed using pre-cold 70% ethanol at 4 ℃, overnight. The next day, centrifuge and discard the supernatant, and wash the cells with PBS twice. Then add the propidium iodide (PI) staining solution (C1052, Beyotime Biotechnology, shanghai, China) and incubate cells at room temperature for 15 min. Then go for the flow cytometric analysis. For cell apoptosis, the DKC1 knockdown A549 and PC-9 cells and control cells were harvested for apoptosis markers (P21 and γH2A.X) analysis using western blot.
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