The designed DNA sequences were synthesized and purified by GenScript Biotech Co., Ltd. (Nanjing, China). DNA strands modified with biotin were purified by High Performance Liquid Chromatography (HPLC), and other strands were purified by economic PAGE (ePAGE) or PAGE. The DNA strands are shown in Figure S1 . All sequences are shown in Table S1 . The concentration of each strand was estimated by measuring the UV absorbance at the wavelength of 260 nm using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, USA). STV (used without further purification), agarose, and GelRed were purchased from Sangon Bio-tech Co., Ltd. (Shanghai, China). NiCl2 was purchased from Sinopharm Chemical Reagent Co., Ltd., Shanghai, China. All aqueous solutions were prepared with ultrapure water.
Agarose
Manufactured by Sangon
Sourced in China
Agarose is a purified polysaccharide derived from red seaweed. It is a common gel matrix material used in electrophoresis techniques for the separation and analysis of macromolecules such as DNA, RNA, and proteins.
Automatically generated - may contain errors
Lab products found in correlation
4s red plus nucleic acid stain, by Sangon (3 mentions)
Fetal bovine serum (fbs), by Thermo Fisher Scientific (3 mentions)
Gelred, by Sangon (2 mentions)
Smart race cdna ampli cation kit, by Takara Bio (2 mentions)
Takara agarose gel dna puri cation kit ver 2, by Takara Bio (2 mentions)
Pmd19, by Takara Bio (2 mentions)
Rnaiso plus, by Takara Bio (2 mentions)
Nanodrop 2000, by Thermo Fisher Scientific (2 mentions)
Nebuffer 2, by New England Biolabs (2 mentions)
Taq dna polymerase, by Sangon (2 mentions)
Te buffer, by Sangon (2 mentions)
Tae buffer, by Sangon (2 mentions)
Sanprep column dna gel extraction kit, by Sangon (2 mentions)
Tris 2 carboxyethyl phosphine hydrochloride tcep, by Sinopharm (2 mentions)
Nanodrop 2000 spectrophotometer, by Thermo Fisher Scientific (2 mentions)
Penicillin, by Thermo Fisher Scientific (2 mentions)
Hoechst 33342, by Thermo Fisher Scientific (2 mentions)
Nicl2, by Sinopharm (1 mentions)
Tetraethyl orthosilicate, by Merck Group (1 mentions)
Ssdnas, by Sangon (1 mentions)
33 protocols using agarose
1
DNA Sequence Synthesis and Purification
2
Cloning and Characterization of Novel Gene
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Total RNA was isolated from the liver tissues by using RNA isoPlus (TaKaRa, Japan). Quantities and qualities of isolated RNAs were measured by electrophoresis and spectrophotometry (Nanodrop 2000, Thermo Scienti c, USA). Following the method of the SMART™ RACE cDNA ampli cation kit (Clontech, USA), the RNA obtained was completely reverse-transcribed into cDNA, which was next used to clone the gene.
A pair of universal ampli ed primers was designed (Table S1), depending on the multiple sequences alignments of numerous species including zebra sh (Barchydanio rerio var), common carp (Cyprinus carpio), roughskin sculpin (Trachidermus fasciatus), yellow cart sh (Pseudobagrus fulvidraco), etc. The PCR program was set as follow: initial denaturing for 5 min at 95°C, 35 cycles of 30 s at 95°C, 30 s at 55°C and 18 s at 72°C, and extra elongation for 5 min at 72°C. The PCR products were collected with 2% agarose (Sangon, China) and then puri ed with a TaKaRa agarose Gel DNA Puri cation Kit Ver.2.0 (TaKaRa). After puri cation, the DNA fragments were ligated into PMD19 (TaKaRa) and the randomly selected positive transformants were opted and sequenced (Invitrogen, China).
A pair of universal ampli ed primers was designed (Table S1), depending on the multiple sequences alignments of numerous species including zebra sh (Barchydanio rerio var), common carp (Cyprinus carpio), roughskin sculpin (Trachidermus fasciatus), yellow cart sh (Pseudobagrus fulvidraco), etc. The PCR program was set as follow: initial denaturing for 5 min at 95°C, 35 cycles of 30 s at 95°C, 30 s at 55°C and 18 s at 72°C, and extra elongation for 5 min at 72°C. The PCR products were collected with 2% agarose (Sangon, China) and then puri ed with a TaKaRa agarose Gel DNA Puri cation Kit Ver.2.0 (TaKaRa). After puri cation, the DNA fragments were ligated into PMD19 (TaKaRa) and the randomly selected positive transformants were opted and sequenced (Invitrogen, China).
3
HPV-6 LAMP Detection Using Silica Nanoparticles
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Iron (III) chloride hydrate (FeCl3•6H2O), ethylene glycol, sodium acetate, ammonium hydroxide, primers of HPV-6 and agarose were purchased from Sangon Biotech. (Shanghai); tetraethyl orthosilicate (TEOS) and (3-aminopropyl) triethoxysilane (APTES) were obtained from Sigma-Aldrich (USA); and Loopamp DNA amplification kit was obtained from Rongyan Biochemistry Company. DNA extraction kit was purchased from Tellgen Life Science (Shanghai, China). Clinical samples of HPV are collected from Shanghai Tenth People’s Hospital. Deionized water with 18 MΩ· cm was used for the whole experiment. The primers of HPV-6 for LAMP amplification were designed on account of the HPV-6 sequences benefit from Primer Explorer V4 Software (Fujitsu, Tokyo, Japan). Nucleic Acid genotyping Kit for Human Papillomavirus was obtained from Topview Life Technology (Shanghai, China).
4
Magnetic Bead-Based CRISPR Detection
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Monodispersed Magnetic Streptavidin Microspheres (MBs) were purchased from Tianjin Bessel Chromatography Technology Development Center (Tianjin, China), with a solid content of 0.5% (w/v) and a particle size of 300 nm. ZEN, Ochratoxin a (OTA), Fumonisin (FB1), Aflatoxin B1 (AFB1) and Aflatoxin M1 (AFM1) were bought form Meizheng Testing Technology Co., Ltd. (Beijing, China). EnGen LbaCas12a from Lachnospiraceae bacterium ND2006 was purchased from New England Biolabs (Ipswich, MA, USA). CRISPR RNA (crRNA) and other ssDNAs were purchased from Sangon Biotech Co., Ltd. (Shanghai, China). Sequence details are given in Table S1 . The buffer solution 1 was used as a reaction solution for the streptavidin-modified magnetic beads and DNA. The CutSmart Buffer and NEBuffer™ 2.1 was from New England Biolabs. Buffer components are visible in Table S2 . PBS, agarose, 50 × TAE, 5 × TBE, EDTA, 30% acrylamide solution (ACR-BIS, 29:1), tetramethylethylenediamine (TEMED), PAGE coagulant, ammonium persulfate (APS)+, 6× loading buffer and DNA Marker were purchased from Sangon Biotechnology Co., Ltd. (Shanghai, China). RNase-free water was employed as the solvent throughout the experiment. All chemical reagents were of analytical grade.
5
Efficient CRISPR-Cas12a Genome Editing Protocol
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EnGen Lba Cas12a (cpf1), NEbuffer2.1, and TEbuffer were all purchased from New England Biolabs (Ipswitch, MA). All DNA sequences as well as g-RNA sequences were synthesized by Sangon Biotech (Shanghai, China) and the sequences are shown in Table S1 . The storage lifetime of cpf1 is 6 months under −20 °C, the g-RNA sequences should be stored at −80 °C no more than 1 month, and all the DNA sequences can be stored at −20 °C for 3 months. DEPC water was also obtained from Sangon Biotech. HAuCl4·4H2O (10 mg/mL) and adenosine (99.9%)were provided by Macklin biotech (Shanghai, China). Agarose, 1*TAE solution, Gelstain dye, loading buffer (6%), and marker (20–500 bp) were all purchased from Sangon Biotech (Shanghai, China). All the chemical reagents used in this work are analytical grade.
6
CTAB DNA Extraction and PCR Analysis
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PCR instrument: MJ Research PTC-200 Peltier Thermal Cycler (Bio-Rad company), Tprofessional standard Thermocycler (Biometra company) and Light Cycler® 96 System (Roche company); Mikro 120 type microcentrifuge (Hettich company); BG-Power 600k electrophoresis apparatus (Beijing Baijing Biotechnology Co., Ltd.); automatic gel imaging analyzer (Beijing Baijing biotechnology limited company); UV-2102 PCS type ultraviolet visible spectrophotometer [Unique (Shanghai) Instrument Co. Ltd.]; WH-3 type vortex oscillator (Shanghai Huxi analytical instrument Factory Co. Ltd.); SYQ-DSX-280B type portable stainless steel autoclave (Shanghai Shenan medical instrument factory).
2×CTAB extract; ethidium bromide (EB); Taq DNA Polymerases (Shanghai Sangon bioengineering Co., Ltd.): Hot start Taq DNA polymerase, Taq DNA Polymerase, and Taq Plus DNA Polymerase; dNTPs. DNA marker (100bp to 600bp); and agarose (Shanghai Sangon bioengineering Co, Ltd.). Other related reagents were molecular biology grade or analytically pure.
2×CTAB extract; ethidium bromide (EB); Taq DNA Polymerases (Shanghai Sangon bioengineering Co., Ltd.): Hot start Taq DNA polymerase, Taq DNA Polymerase, and Taq Plus DNA Polymerase; dNTPs. DNA marker (100bp to 600bp); and agarose (Shanghai Sangon bioengineering Co, Ltd.). Other related reagents were molecular biology grade or analytically pure.
7
DNA Extraction of Dian-Jixueteng and Jixueteng
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A total of nine commodity samples retailed as Dian-Jixueteng and Jixueteng were purchased from different pharmacies in Yunnan and Guangdong provinces [Table 1 ]. Cetyltrimethylammonium bromide (CTAB), NaCl, ethylenediaminetetraacetic acid (EDTA), chloroform, isopropanol, isoamyl, and mercaptoethanol were analytical grade and manufactured by Tianjin Zhiyuan Chemical Reagent Factory (Tianjin, China). Polyvinylpyrrolidone (PVP), Tris-HCl buffer (pH 8.0), TE buffer, TAE buffer, agarose, Taq PCR Master Mix (×2, blue dye), and SanPrep Column DNA Gel Extraction Kit were purchased from Sangon Biotech (Shanghai, China). Goldview (MYM Biological Technology Co., Ltd., USA) was used for agarose gel electrophoresis.
8
Characterization of Lywallzyme and Driselase
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Lywallzyme was purchased from the Guangdong culture collection center. Driselase was purchased from Sigma-Aldrich, Inc. Mannitol, anthracone, and agarose, analytically pure, were purchased from Sangon Biotech (Shanghai) Co., Ltd. Alternative random primers were synthesized by Sangon Biotech (Shanghai) Co., Ltd. Sulfuric acid (analytically pure) and potassium bromide (spectroscopically pure) were bought from the Sinopharm Chemical Reagent Co., Ltd. The DNAsecure Plant Kit (DP320) was purchased from Tiangen Biotech (Beijing) Co., Ltd. A phosphoglucomutase (PGM) Elisa Kit and glucose phosphate isomerase (GPI) Elisa Kit were purchased from Fu Life Industry Co., Ltd. (Shanghai).
9
HSV-1 Plaque Assay Protocol
10
Blood Collection and DNA Extraction
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Collect 3 ml of peripheral venous blood from all newly diagnosed patients before chemotherapy and from healthy subjects into EDTA anticoagulant tubes. Centrifuge, discard the supernatant and store in a refrigerator at −80°C. Agarose was purchased from Sangon Biotech (Shanghai), Trans2K DNA Marker and 2 × EasyTaq PCR SuperMix (+dye) were purchased from TransGene Biotech; DNA extraction kit was purchased from Genenode.
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