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9 protocols using isopropanol

1

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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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

Plant DNA and RNA Extraction for Viral Detection

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Total DNA was extracted with cetyl-trimethyl-ammonium bromide (CTAB) (Sangon Biotech, China). Briefly, leaf samples were first ground and mixed with CTAB solutions containing 2% β-mercaptoethanol (Sigma, Saint Louis, MO, USA). Next, these samples were incubated at 65 °C and then trichloromethane (Sangon Biotech, China) was added. Samples were then centrifuged, upper phase was collected and mixed with isopropanol (Sangon Biotech, China). DNA was obtained by centrifugation and washing with 75% ethanol solution. Total RNA was extracted using TRIzol (Ambion, Austin, TX, USA). Samples were first ground and mixed with TRIzol. Trichloromethane was added and samples were then centrifuged. Supernatants were collected and mixed with isopropanol. After washing with ethanol solution, RNA was obtained by centrifugation. For the quantification of begomoviruses and betasatellites in DNA samples, SYBR Green Premix Pro Taq HS qPCR Kit (Accurate Biology, Changsha, China) and CFX96 Real-Time PCR Detection System (Bio-Rad, Hercules, California, USA) were used. For the analysis of gene expression level of AV1 and βC1, cDNA was synthesized using Evo M-MLV RT Kit with gDNA Clean for qPCR (Accurate Biology, China). QPCR was then performed as mentioned above. Primers are listed in Table 1.
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5

Optimized Biomolecule Extraction Protocols

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Ethylene diamine tetraacetic acid (EDTA), cetyltrimethylammonium bromide (CTAB), sodium dodecyl sulfate (SDS), Tris-HCl, NaCl, urea, Na2CO3, NaHCO3, sodium citrate (C6H5Na3O7), guanidine isothiocyanate (C2H6N4S), sodium N-dodecanoylsalcosinate (C15H10NO4Na), β-mercaptoethanol, alcohol, isoamyl alcohol, and isopropanol were purchased from Sangon Biotech (Shanghai, China). HAuCl4 was purchased from Sinopharm (Shanghai, China). Bovine serum albumin (BSA), sucrose, and alginate were obtained from Meilunbio Biotech (Dalian, China). Absorbent pads (CH27) and sample pads (SB06) were purchased from KinBio Biotech (Shanghai, China). The gold absorbent pad (GL0194), PVC backing plate (DB-6), and nitrocellulose membrane (Millipore 135) were obtained from Jiyi Biotech (Shanghai, China). PCR Master Max and the anti-5-FAM antibody were obtained from BBI Biotech (Shanghai, China). Streptavidin and biotin-BSA were obtained from Solarbio Biotech (Beijing, China).
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6

Hydrogel Synthesis and Characterization

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Sodium alginate (SA), N,N’-methylenebisacrylamide (MBAA), N,N,N,N-tetramethylethylenediamine (TEMED), and calcium sulfate dihydrate (CaSO4·H2O) were purchased from Adamas. Ammonium persulfate (APS), (3-aminopropyl)triethoxysilane (APTES), 3-(trimethoxysilyl)propyl methacrylate (TMSPMA), 1,6-hexamethylenediamine (HMDA) and benzophenone (BP) were purchased from Aladdin. Potassium chloride was purchased from Rhawn. Acrylamide (AM) was purchased from General Reagent. Glycerol and methanol were purchased from Damao. Poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT:PSS) was purchased from Bidepharm. Isopropanol was purchased from Sangon Biotech. Ethanol was purchased from Chemical Reagent. All chemicals were used as received without further purification.
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7

Adipocyte Lipid Quantification Protocol

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The mature adipocytes were grown on a coverslip and fixed with 10% formalin (Guangzhou Dingguo Biology, Guangdong, China) at room temperature for 1 h. After fixation, the cells were washed once with 60% isopropyl alcohol (Sangon Biotech, Shanghai, China). Oil Red O solution (Sangon Biotech, Shanghai, China) was prepared according to the manufacturer’s instructions and added to the plate for 1 h. The coverslips were then visualized under a microscope. The cell culture plates were treated with isopropanol (Sangon Biotech, Shanghai, China), and lipid accumulation was determined according to absorbance at 510 nm.
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8

Gene Expression Analysis Protocol

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One milliliter of TRI Reagent® (Sigma, St. Louis, MO, USA) was applied to dissociate the specimens and cells. Isopropanol (Sangon Biotech, Shanghai, China) was used to precipitate the total RNA. After measuring the concentration of RNA with a spectrophotometer (Tiangen, Peking, China), 1000 ng of total RNA was reverse transcribed to cDNA, and then, 1 µl cDNA was employed to conduct quantitative PCR (polymerase chain reaction) following the instructions of the manufacture (GeneCopoeia, Rockville, MD, USA). The specific primers of CREB1, CCAR1, JNK1, GAPDH, miR-433 and snRNA U6 were also purchased from GeneCopoeia. The 2-△△CT method was adopted to analyze the relative expression.
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9

CLA Extraction from Fermentation Culture

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After the flask culture stage, CLA was extracted from the culture as follows. Four milliliters of the fermentation supernatant components was transferred to a clean centrifuge tube, and C17:0 heptadecanoic acid (Sigma), as an internal standard, was added to a final concentration of 233 µg/mL in each sample. Four milliliters of isopropanol (Sangon Biotech) was added to the solution and then vortexed for 30 s, and then 4 mL of n-hexane (Sangon Biotech) was added into this mixture and vortexed for 30 s. The sample was centrifuged at 3,913 × g for 5 min. The n-hexane layer was transferred into a clean fat-extracting bottle and dried off under a nitrogen stream.
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