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69 protocols using methanol

1

Isolation and Characterization of Ginseng-Associated Bacteria

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Rhizosphere soil adhering to the roots of P. ginseng was collected from a ginseng-cultivated eld in Jilin, China (E: 126.85°, N: 42.39°) (Fig. S1 in Additional le 3). The ingredients used to create the mineral salt medium (MSM) have been previously described by Wang et al. [12] . The genomic DNA of bacterial strain was extracted and puri cation by Genomic DNA Puri cation Kit (Tiangen, Beijing, China). The phydroxybenzoic acid (99% purity) was procured from the Sinopharm Chemical Reagent Co., Ltd.
(Shanghai, China). Ultra-high performance liquid chromatography (UPLC) grade formic acid and methanol were obtained from CNW Technologies GmbH (Dusseldorf, Germany). Other chemical reagents were analytical grade and were purchased from local suppliers.
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2

Comprehensive Metabolic Profiling Protocol

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The equipment and reagents used in this study included: High Resolution Mass Spectrometer (QE Plus, Thermo Fisher Technologies, Waltham, MA, United States), PCR Amplifier (580BR10905, Bio-Rad, Hercules, CA, United States), Bioanalyzer (2100, Aglient, Santa Clara, CA, United States), NanoDrop (2000, Thermo Fisher, Waltham, MA, United States). High performance liquid chromatography (Dionex U3000 UHPLC, Thermo Fisher Technologies, Waltham, MA, United States). A chromatographic column, (100 mm × 2.1 mm, 1.8 μm), was purchased from Waters (ACQUITY UPLC HSS T3, Milford, MA, United States). A DNeasy PowerSoil Kit (Cat. No. 12888) and QIAamp 96 PowerFecal QIAcube HT kit (Cat. No. 51531) was purchased from QIAGEN (Germantown, MD, United States). Qubit dsDNA Assay Kit (Cat. No. Q32854) was purchased from Life Technologies (Eugene, OR, United States). A Tks Gflex DNA Polymerase (Cat. No. R0608) was purchased from Takara (Dalian, China). All chemicals and solvents were analytical or HPLC-grade. Water, methanol, acetonitrile, and formic acid were purchased from CNW Technologies GmbH (Düsseldorf, Germany). L-2-chlorophenylalanine was purchased from Shanghai Hengchuang Biotechnology Co., Ltd. (Shanghai, China).
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3

High-Purity Chemical Analysis Protocol

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All chemicals and solvents were high-performance
liquid chromatography (HPLC) or analytical grade. Formic acid, acetonitrile,
methanol, and ammonium bicarbonate were purchased from CNW Technologies
GmbH (Düsseldorf, Germany). The water used was doubly deionized
using MilliQ Ultra purification system (Millipore, Vimodrone, Italy).
L-2-Chlorophenylalanine was purchased from Heng Chuang Biotechnology
Co., Ltd. (Shanghai, China).
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4

Microbial Compound Extraction and Analysis

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The companies names, cities and countries of used chemicals as followed: methanol (85%), benzene, distilled water and ethanol (70%) from CNW Technologies GmbH (Dusseldorf - Germany). Aluminum chloride from Sangon Biotech (Shanghai- China). Sodium nitrite, sodium bicarbonate and sodium hydroxide from Research Lab Fine Chem. Industries (Maharashtra - India). Dimethyl sulfoxide (DMSO) from Piochem (Giza - Egypt). Gentamycin, when agar from Himedia (Giza - Egypt). Folin-Ciocalteau from Sigma Aldrich (USA). The speacies was authenticated at fungi center, Al-Azhar University (Nasr city - Egypt).
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5

Analysis of Organic Compounds by GC-MS

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All chemicals and solvents were analytical or HPLC grade. Water, methanol, pyridine, n-hexane, methoxylamine hydrochloride (97%), and bis (trimethylsilyl) trifluoroacetamide (BSTFA) with 1% trimethylchlorosilane (TMCS) were purchased from CNW Technologies GmbH (Düsseldorf, Germany). Trichloromethane was obtained from Sinopharm Chemical Reagent Co.; Ltd. (Shanghai, China). L-2-chlorophenylalanine was obtained from Shanghai Hengchuang Biotechnology Co.; Ltd. (Shanghai, China).
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6

Mesalazine Colitis Treatment Protocol

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Mesalazine was purchased from Shanghai Haoyuan Biomedical Technology Co., Ltd. (Shanghai, China); TNBS and formic acid were purchased from Sigma-Aldrich (St. Louis, MO, USA); methanol and acetonitrile were purchased from CNW Technologies (Shanghai, China); 2-chloro-L-phenylalanine was purchased from Shanghai Hengbai Biotech Co., Ltd. (Shanghai, China); and enzyme-linked immunosorbent assay kits were purchased from Nanjing Jiancheng Bioengineering Institute (Nanjing, Jiangsu, China).
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7

Quantitative Analysis of Bioactive Compounds

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LC-MS grade acetonitrile, methanol, ammonium acetate, and formic acid were purchased from CNW Technologies (Duesseldorf, Germany). 2-Chloro-L-phenylalanine was purchased from Shanghai HB Biotech Co., Ltd. (Shanghai, China). Deionized water was prepared on a Millipore Milli-Q water purification system (Billerica, MA, USA). Apigenin was obtained from China National Engineering Research Centre for Solid Preparation Manufacturing Technology (Beijing, China). Psoralen was purchased from China Food and Drug Control Institute (Beijing, China). Assay kits for aminotransferase (ALT) and aspartate aminotransferase (AST) were purchased from Nanjing Jiancheng Biological Engineering (Nanjing, China). RFH was purchased from Baining Pharmaceutical Co., Ltd. (Guangzhou, Guangdong).
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8

Standardized Metabolic Profiling Protocol

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The SWP products were generously provided by Hunan Jiudian Pharmaceutical Co., Ltd. (Hunan, China). In order to obtain reliable experiment results, the preparation and quality control (QC) of SWP were monitored according to our previous research.6 (link) 2-Chloro-L-phenylalanine, as internal standards for metabolomics analysis, was purchased from Shanghai HC Biotech Co., Ltd. (Shanghai, China) and Avanti (USA) respectively. Q-Exactive LC-MS/MS (Thermo Fisher Scientific) Acetonitrile, methanol, formic acid and LC-MS grade water were purchased from CNW Technologies GmbH (Düsseldorf, Germany).
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9

Quantitative LC-MS Analysis Protocol

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Methanol and acetonitrile were purchased from CNW Technologies, acetic acid from Fisher Chemical, and ammonium acetate from Sigma-Aldrich (Shanghai, China). All reagents were of LC-MS grade. Ultra-high-performance liquid chromatography was performed using Q Exactive HFX High-Resolution Mass Spectrometry (Heraeus Fresco Model 17 Centrifuge; Thermo Fisher Scientific, Waltham, MA, USA). A scale (model BSA124S-CW) was purchased from Sartorius. A Ps-60al ultrasonic instrument was purchased from Shenzhen Redbond Electronics Co., Ltd. A rice cooker (Mb-wfs4029 Midea) was purchased from Midea Life Electric Appliance Manufacturing Co., Ltd. (Foshan, China).
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10

Immunological Effects of Hypothyroidism in Mice

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4-6 weeks old healthy female KM mice (SPF grade) with body weights of 16-18 g were purchased from Ji’nan Pengyue Laboratory Animal Breeding Co., Ltd (Shandong, China). The mice were housed in a clean room at a temperature of 23 ± 2°C and humidity of 50 ± 5% with a 12 h alternating light and dark cycle. They were permitted free access to food and water. All animal experiments were performed according to the National Institutes of Health Guidelines for the Care and Use of Laboratory Animals and were approved by the Animal Care and Use Committee of Shandong Province, China. The thyroxine tablets were purchased from Shandong Renhe Pharmaceutical Co., Ltd (China). PerCP-Cy™5.5 Hamster Anti-Mouse CD3e (Cat# 551163), FITC Rat Anti-Mouse CD4 (Cat# 553047), APC-H7 Rat anti-Mouse CD8a (Cat# 560182), PE Rat Anti-Mouse IFN-γ (Cat# 554412), Leukocyte Activation Cocktail, with BD GolgiPlug (Cat. No.550583) were purchased from BD Pharmingen™. All chemicals and solvents were analytical or HPLC grade water, methanol, acetonitrile, formic acid, pyridine, n-hexane, methoxylamine hydrochloride, N, O-Bis (trimethylsilyl) trifluoroacetamide (BSTFA) with 1% chlorosilane were purchased from CNW Technologies GmbH (Germany), L-2 chlorophenylalanine was from Shanghai Hengchuang Bio technology Co Ltd. (China).
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