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15 protocols using ethanol

1

Reagents for Biomolecular Modification

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5-Fluorodeoxyuridine was purchased from Alfa Aesar (Shanghai, China). 4,4ʹ-Dimethoxytrityl Chloride (DMT-Cl, 97%) N,N-Diisopropylethylamine (DIPEA, 97%) and 2-Cyanoethyl N,N,N’,N’-tetraisopropylphosphordiamidite (95%) were obtained from Macklin Inc. (Shanghai, China). N-(ε-malemidocaproyloxy) succinimide ester (EMCS) was purchased from Aladdin (Shanghai, China). Ni-NTA agarose, and Sephadex G-25 were obtained from GE Healthcare (Piscataway, USA). Imidazole, sodium chloride, sodium acetate, polyacrylamide, tris base, acetic acid, ethylenediaminetetraacetic acid (EDTA), magnesium chloride, ethanol, and DAPI were obtained from Sangon Biotech (Shanghai) Co., Ltd (China). Amicon ultracentrifugal filters were purchased from Merck Millipore Ltd (Darmstadt, Germany). RPMI 1640 medium, DMEM medium, MEBM medium, trypsin, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT), antibiotic-antimycotic (100×) and fetal bovine serum (FBS) were purchased from Wisent Biotechnology (Nanjing) Co. Ltd (China). All chemicals were used without further purification.
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2

E. coli Growth and Genetic Manipulation

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E. coli K-12 strains (SI Appendix, Table S1) were grown aerobically at 37 °C in LB medium (63 (link)) with shaking at 200 rpm. Colony formation was on LB agar at 37 °C. Bacteriophage P1-mediated transduction (64 ) or CRISPR-based allelic exchange (24 (link)) was used for strain construction. Flow cytometry reagents were purchased from Becton Dickinson. Tryptone, yeast extract, powder for LB broth and agar, and carboxy-H2DCFDA were obtained from Thermo Fisher Scientific. Other reagents, including antimicrobials (ciprofloxacin, oxolinic acid, kanamycin, ampicillin, tetracycline, moxifloxacin, and chloramphenicol), phenol, dimethyl 2-oxoglutarate, cyclic AMP, sodium pyruvate, and DMSO were purchased from Sigma-Aldrich. Gentamicin, amikacin, hydrogen peroxide, chlorhexidine, ethanol, isopropanol, 1-butanol, potassium dichromate, sodium hypochlorite solution (5.2%), hydrogen chloride, and sodium hydroxide were purchased from Sangon Biotech. Meropenem (Shenghuaxi Pharmaceutical) and ceftriaxone (Roche) were from Zhongshan Hospital (Xiamen, China) pharmacy.
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3

Diverse Microbial Sample Collection and Preparation

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Actual samples including throat swabs collected from the patients diagnosed with Mycoplasma pneumoniae infection, human papilloma virus type 16 (HPV-16) positive cervical swabs, as well as gastric mucosa of the patients suffering severe stomachache with suspected Helicobacter pylori infection were provided by the Affiliated Hospital of Qingdao University. All the samples were immediately stored at −20 °C after collection for subsequently use. Streptococcus aureus (ATCC 25923), Salmonella typhimurium strains (ATCC 14028) were provided by Navid Biotechnology Co., Ltd (Qingdao, China). SARS-CoV-2 pseudovirus was purchased from Fubio Biological Technology Co., Ltd (Shanghai, China). Guanidine hydrochloride, guanidine isothiocyanate, proteinase K, ethanol, isopropanol, SDS, TritonX-100, Tween-20 and pig serum were purchased from Sangon Biotech Co., Ltd (Shanghai, China). All the other chemicals and reagents were of analytical grade.
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4

Scanning Electron Microscopy of Tea Leaf Wax

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Tea leaves were sliced (1 cm × 1 cm) and soaked in a glutaraldehyde-fixed solution (Beijing Solarbio Science & Technology Co., Ltd., Beijing, China) overnight. After gradient dehydration with 30%, 50%, 70%, and 90% ethanol (Sangon Biotech (Shanghai) Co., Ltd., Shanghai, China), followed by freeze drying and gold spraying, an S-3400N scanning electron microscope (Hitachi Limited Co., Ltd., Tokyo, Japan) was used to observe tea leaf cuticular wax.
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5

Solvothermal Synthesis of ZnO Nanoparticles

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Zinc acetate (Zn(CH3COO)2·2H2O), sodium citrate (Na3C6H5O7·2H2O), sodium hydroxide (NaOH), and ethanol (AR) were purchased from Sangon Biotech (China, www.sangon.com). ZnO was synthesized by a simple one-step method. A total of 0.2195 g of zinc acetate and 0.2941 g of sodium citrate were dissolved in 40 mL of deionized water and magnetically stirred for 10 min to form a clear solution. The above mixed solution was used as a precursor solution. Then, a certain amount of 3 mol/L NaOH solution was added dropwise to the precursor solution, and the PH values of the solutions were adjusted to be 9, 10 and 11. The above mixed solution was transferred to a 100 mL autoclave, sealed, and placed in a constant temperature drying oven at 120 °C for 8 h. It was cooled to room temperature, washed several times with deionized water and absolute ethanol, and placed in a constant temperature drying oven at 60 °C to be dried. We named the samples synthesized under the above three different PH values ZnO-1, ZnO-2, and ZnO-3.
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6

Chymotrypsin-based Protein Digestion

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The chemicals used in the experiments before the digestion (calcium chloride and ethanol) were purchased from Sangon Biotech Co. Ltd, Shanghai, China. Chymotrypsin was supplied by Thermo Fisher Scientific. MeOH and FA were purchased from Sigma—Aldrich (St. Louis, MO).
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7

Artificial Aging of Vegetable-Tanned Leather

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The new vegetable tanned cattle leather was collected from the market (Houjie Dingtai Leather Company, Dongguan, China).
The required reagents for the artificial aging experiments include hydrochloric acid (HCl), ammonium bicarbonate (NH4HCO3), and sodium hydroxide (NaOH). All reagents are of analytical grade and were obtained from Sangon Biotech (Shanghai, China) Co., Ltd.
For the orthogonal experiments, the following reagents were used: NaOH (analytical grade, Sangon Biotech) and a protein concentration determination kit (Sangon Biotech).
The reagents used for electrophoresis experiments include precast gels, protein loading buffer, electrophoresis running buffer, protein maker, ethanol, methanol, acetic acid, ammonium sulfate, and Coomassie brilliant blue G250. All reagents are of analytical grade and were purchased from Sangon Biotech.
For the biomass spectrometry experiments, the required reagents include formic acid (chromatography grade, Sigma, St. Louis, MO, USA), acetonitrile (chromatography grade, Sigma), and trypsin (sequencing grade, Promega, Madison, WI, USA).
All reagents used in these experiments are of high purity and were procured from reputable suppliers. The quality of the reagents ensures the reliability and accuracy of the experimental results.
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8

Synthesis and Characterization of EMCS-Pt Conjugate

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The DNAs were synthesized from Sangon Biotech (Shanghai) Co., Ltd. N-(ε-maleimidocaproyloxy)succinimide ester (EMCS) and cis-platinum was purchased from Aladdin (Shanghai, China). Ni-NTA agarose and Sephadex G-25 were obtained from GE Healthcare (Piscataway, NJ, USA). Imidazole, sodium chloride, sodium acetate, polyacrylamide, trizma base, acetic acid, ethylenediaminetetraacetic acid (EDTA), magnesium chloride, ethanol, sodium diethyldithiocarbamate (DDTC) and DAPI were obtained from Sangon Biotech (Shanghai) Co., Ltd. Amicon® ultracentrifugal filters were purchased from Merck Millipore Ltd. (Darmstadt, Germany). Gibco® RPMI 1640 medium, trypsin, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT), dimethylsulfoxide (DMSO), antibiotic–antimycotic (100×), fetal bovine serum (FBS), and DAPI were purchased from Thermo Fisher Scientific (Waltham, MA, USA). All chemicals were purchased and used without further purification.
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9

Total RNA Extraction and Evaluation

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Total RNA was extracted from cells using Transzol (TaKaRa, Japan), chloroform (Sangon, Shanghai, China), isopropyl alcohol (Sangon, Shanghai, China), DEPC water (Sangon, Shanghai, China) and 75% ethanol (Sangon, China). The yield of RNA was determined using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA), and the integrity was evaluated using agarose gel electrophoresis stained with ethidium bromide.
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10

Total RNA Isolation and RT-qPCR Analysis

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For total RNA isolation, Trizol (Invitrogen, Carlsbad, CA, USA), chloroform (China sinopharm, Shanghai, China) and isopropanol (Sangon biotech, Shanghai, China) were added into irradiated cells, subsequently followed by 75% ethanol (China sinopharm) rinsing. The reverse transcription reaction system was performed according to the manufacturer’s protocol of the PrimeScript RT Master Mix kit (Takara, Tokyo, Japan). The synthesized cDNA samples were amplified and detected in the RT-qPCR system under the instruction of TB Green Premix Ex Taq II kit (Takara) in QuantStudio 6 (Thermo) (Tables S1–S5, RT-qPCR protocol).
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