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69 protocols using acetonitrile

1

Characterization of Extract Components

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Analysis of the properties of the components contained in the extract was performed with an Agilent 1260 Infinity (Agilent Technologies, Santa Clara, CA, USA) ODS column (Cadenza CD-C18 column, 250 × 4.6 mm, particle size 3 µm, Imtakt Corporation, Kyoto, Japan) at a constant temperature of 40 °C. In the mobile phase, a 5-fold-diluted extract in ethanol of 30 µL was applied to the column, and elution was performed at a flow rate of 1 mL/min with a mixture of solvents A (0.4% formic acid (Fujifilm Wako Pure Chemicals, Osaka, Japan)) and B (100% acetonitrile (Kanto Chemical, Tokyo, Japan)). Elution was performed under the following conditions: gradient from initial conditions to 40 min (0 min (A:B = 93:7), 33 min (A:B = 60:40), 40 min (A:B = 0:100)), from 40 to 70 min (A:B = 0:100). Spectra were detected with a diode array detector (DAD) at 280 and 326 nm. In parallel with the analysis, fraction collection was also performed. The preparative schedule was as follows: Fr.1: 8–15 min, Fr.2: 19–25 min, Fr.3: 42–51 min, Fr.4: 51–60 min, Fr.5: 60–69 min.
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2

Isolation and Characterization of Mitochondria

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Isoflurane, benzophenone, mannitol (D-mannitol), a Cholesterol E-Test Kit, and DDC were purchased from Wako Pure Chemical Industries, Ltd. (Osaka, Japan). DIS powder and 2-hydroxypropyl-β-cyclodextrin (HPCD) were kindly donated by Ouchi Shinko Chemical Industrial Co., Ltd. (Tokyo, Japan) and Nihon Shokuhin Kako Co., Ltd. (Tokyo, Japan), respectively. A Mitochondrial Isolation kit, a Cytochrome c Oxidase Assay kit, and an ATP Bioluminescent Assay kit were purchased from Sigma Aldrich Japan (Tokyo, Japan). A Bio-Rad Protein Assay kit was provided by BIO-RAD (California, USA). We obtained 0.5% phenylephrine and 0.5% tropicamide from Santen Pharmaceutical Co., Ltd. (Osaka, Japan). An ELISA Insulin Kit and an RNA PCR Kit (AMV Ver 3.0) were purchased from Morinaga Institute of Biological Science Inc. (Kanagawa, Japan) and Takara Bio Inc. (Shiga, Japan), respectively. Methylcellulose type SM-4 (MC) was obtained from Shin-Etsu Chemical Co., Ltd. (Tokyo, Japan). Pentobarbital was provided by Sumitomo Dainippon Pharma Co., Ltd. (Toyo, Japan). Benzalkonium chloride (BAC), methanol, and acetonitrile was purchased from Kanto Chemical Co., Inc. (Tokyo, Japan). LightCycler FastStart DNA Master SYBR Green I was provided by Roche Diagnostics Applied Science (Mannheim, Germany). All other used chemicals were of the highest purity commercially available.
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3

Synthesis and Characterization of Polymers

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Acetone, hexane, tetrahydrofuran (THF), methanol, chloroform, ethyl acetate (EtOAc), ethanol, acetonitrile, acryloyl chloride, sodium hydroxide, potassium hydroxide, N, N-dimethylformamide (DMF), anhydrous magnesium sulfate, and diethyl ether were purchased from Kanto Chemical. Copper (I) chloride (CuCl), lithium bromide (LiBr), ethylamine, and DIBOD were purchased from the Tokyo Chemical Industry. Sodium azide and dibenzocyclooctyne-amine (DBCO-amine) were purchased from Sigma-Aldrich. N, N-dimethylformamide (DMF) for preparing the GPC/SEC’s eluent and hydrochloric acid (12 N) were purchased from FUJIFILM Wako Pure Chemical Industry. Pentaerythritol tetra (2-chloropropionate) (PETCP) was commercially obtained as a custom-made product from the Tokyo Chemical Industry and used as an initiator. Ultrapure water (specific resistance value: 18.2 MΩ cm) obtained by purifying tap water with a Direct-Q 3UV manufactured by Millipore was used. In addition, N-isopropyl acrylamide (NIPA) and tris (2-dimethylamino ethyl) amine (Me6TREN) were kindly provided by Kohjin and Mitsubishi Chemical, respectively. NIPA was purified by recrystallization using a mixture of hexane and Acetone. Me6TREN (Mitsubishi Chemical) and DMF (Kanto Chemical) for synthesis were purified by vacuum distillation. Furthermore, other chemicals were used without purification.
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4

Bioactive Lipid Standards Characterization

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LC/MS-grade water, acetonitrile, methanol, and 2-propanol were purchased from Kanto Chemical Co, Inc (Tokyo, Japan). LC/MS-grade ammonium acetate was purchased from Merck (Darmstadt, Germany). LC/MS-grade acetic acid was purchased from Fujifilm Wako Pure Chemical Co (Osaka, Japan). Standards were obtained from Nacalai Tesque, Inc (Kyoto, Japan), Fujifilm Wako Pure Chemical Co, and Merck. Stable isotope-labeled standards were obtained from Cayman Chemical Co (Ann Arbor, MI), Cambridge Isotope Laboratories, Inc (Tewksbury, MA), Steraloids Inc (Newport, RI), Avanti Polar Lipids Inc (Alabaster, AL), and Merck. Compound names and abbreviations of the 144 bioactive lipid standards used in this study are listed in supplemental Table S1.
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5

Aniline Quantification Analytical Protocol

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Reagent 1) Aniline standard stock solution (1000 mg/L). The aniline standard (manufactured by Wako Pure Chemical Industries, Ltd.), 100 mg, was a dissolved into 100 mL of methanol.
2) Aniline standard solution for the calibration curve (0.05 -2 μg/L). The aniline standard stock 1 mL had a constant volume of up to 100 mL with Mill-Q water. It was then diluted to 6 steps in the 0.05 -2 μg/L range with Mill-Q water.
3) Aniline-2,3,4,5,6-d5 standard stock solution (100 mg/L: referred to as "aniline-d5"). The aniline-d5 standard (manufactured by Wako Pure Chemical Industries, Ltd.), 10 mg, had a constant volume of up to 100 mL of methanol. This surrogate substance of aniline was used as an internal standard. 4) Mobile phase. Ammonium acetate (Wako Pure Chemical Industries, Ltd., special grade) used in the mobile phase was used. Acetonitrile (Kanto Chemical Co., LC/MS analysis grade) used in the mobile phase was used. The purified water used in the mobile phase was Milli-Q water.
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6

Organic Synthesis of Substituted Benzenes

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4-VA was purchased from Ark Pharm (Illinois, USA). Vinylbenzene, p-bromobenzonitrile (Br-Ph-CN), p-bromoanisole (Br-Ph-OCH3), bromobenzene (Br-Ph-H), p-bromobenzoic acid ethyl ester (Br-Ph-COOEt), p-bromotoluene (Br-Ph-CH3), 4-methoxy-trans-stilbene and 4,4′-dimethoxy-trans-stilbene were from Tokyo Chemical Industries (Tokyo, Japan). 4-TFV were from Oakwood products (South Carolina, USA). Palladium(II) acetate (Pd(OAc)2) and N,N-dimethylacetamide (DMAc) were from Nacalai Tesque (Osaka, Japan). Triethylamine (TEA) was purchased from Wako (Tokyo, Japan). Acetonitrile was from Kanto Chemical (Tokyo, Japan).
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7

Solvent Extraction and Chemical Analysis

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OAm, decane, oxalic acid (99%), silver nitrate (AgNO3, 99.8%), butanol (98.0%), methyl ethyl ketone (99.0%), 1,4-dioxane (>98.0%), pentane (97.0%), tetrachloroethylene (>97.0%), and cyclopentanone (>95.0%) (FUJIFILM Wako Pure Chemical Co., Osaka, Japan); diacetone alcohol (>98.0%), ethylbenzene (>99.0%), ethyl benzoate (>99.0%), butylbenzene (>99.0%), furan (>99.0%), and dimethyl sulfoxide (DMSO) (>99.0%) (Tokyo Chemical Industries, Ltd., Tokyo, Japan); and toluene (>99.5%), acetonitrile (99.5%), acetone (99.5%), cyclohexane (>99.5%), and tetrahydrofuran (>99.5%) (KANTO CHEMICAL Co., Inc., Tokyo, Japan) were used for this study.
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8

Phosphate Buffer Excipient Preparation

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HPMC (METOLOSE®, 90SH-4000, MW: 300,000, viscosity 4000 mPa•s, methoxy group 22.0-24.0%, hydroxypropyl group 8.5-10.5%) and MC (METOLOSE®, SM-1500) were purchased from Shin-Etsu Chemical Co., Ltd, Tokyo, Japan. Sodium dihydrogen phosphate and dihydrate, disodium hydrogen phosphate and 12 hydrates, phosphoric acid, acetonitrile, and purified water were purchased from Kanto Chemical Co., Inc., Tokyo, Japan.
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9

Pyrene Metabolism Profiling Protocol

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Pyrene, PYOH, 3'-phosphoadenosine 5'-phosphoslfate (PAPS), sulfatase (from limpet Type V; 34 U/mg), β-glucuronidase (from bovine liver, Type B-1; 1,240 U/mg), β-glucosidase (from almond; 3.4 U/mg), and bovine serum albumin were obtained from Sigma-Aldrich Co. (St.
Louis, MO). Methanol, acetonitrile, acetic acid, and ammonium acetate were purchased from Kanto Chemical Co., Inc. (Tokyo, Japan). Pyrene-1-sulfate (PYOS) was obtained from TOPU Bio (Toyama, Japan). Uridine-diphosphate-glucuronic acid (UDP-GA) was purchased from Wako (Osaka, Japan). All chemicals used for high-performance liquid chromatography (HPLC) and mass spectrometry (MS) were of HPLC or MS grade, respectively, and were obtained from Kanto Chemical Co. Inc.
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10

Quantitative LC-MS Analysis of Drugs

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LC/MS-grade methanol, acetonitrile and ammonium hydroxide were purchased from Kanto Chemical (Tokyo, Japan). Ammonium bicarbonate (1 mol/L) was purchased from Cell Science & Technology Inst., Inc. (Miyagi, Japan). Ammonium formate (1 mol/L) and LC/MS-grade formic acid were purchased from Fujifilm Wako Chemical Industries (Osaka, Japan). Glutathione (GSH)-13C2, 15N was purchased from Taiyo Nissan Corp. (Tokyo, Japan) and used as internal standard (IS). All drugs were obtained from Senju Pharmaceutical Co., Ltd. (Osaka, Japan), Santen Pharmaceutical Co., Ltd. (Osaka, Japan), Pfizer Japan Inc. (Tokyo, Japan), Kowa Co., Ltd. (Aichi, Japan) or Novartis Pharma K.K. (Tokyo, Japan).
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