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55 protocols using dl2000 dna marker

1

DNA Fragment Separation and Sequence Analysis

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To separate DNA fragments, PCR products prepared above were added into 5% agarose gel with Golden View™ (Takara) and electrophoresed at 120 V for 25 min, together with DL2000 DNA marker (Takara). Bands of nucleic acid product were visualized using a ChemiDoc™ MP imaging system (Bio-Rad). Specific positive products were sequenced by Ruibiotech company in China. The nucleotide sequences were analyzed against sequences deposited in GenBank using BLASTn (https://blast.ncbi.nlm.nih.gov/Blast.cgi) for high similarity analysis of sequences.
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2

Total RNA Extraction and cDNA Synthesis

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Total RNA was extracted from collected petals using a RNAprep Pure Plant Kit (Polysaccharides&Polyphenolics-rich, TIANGEN). RNA quality and purity were checked by 1% agarose gel electrophoresis, using the DL2000 DNA Marker (TaKaRa) as a size indicator. RNA concentrations and ratios of absorbance at 260 nm to that at 280 nm (260/280) were determined using a NanoDrop 1000 spectrophotometer (Implen, Germany). Total RNA was reverse transcribed into cDNA according to the steps of PrimeScript RT reagent Kit with gDNA Eraser (TaKaRa). PCR amplification was conducted in 20 µL reaction mixtures containing 10 µL total RNA of erasing gDNA, 1 μL PrimeScript RT Enzyme Mix 1, 1 µL RT Primer Mix, 4 μL 5× PrimeScript Buffer 2 (for Real Time), and ddH2O to adjust the volume. Cycling conditions were 37°C for 15 min, then 85°C for 5 s.
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3

Sensitive PCR Detection of Toxoplasma gondii in Soil

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The PCR method based on T. gondii-conserved gene internal transcribed spacer 1 (ITS-1) as target gene for soil detection was conducted according to previously reported [6 (link)]. To standardize the sensitivity, diluted T. gondii tachyzoites at the concentration of 1 × 105, 1 × 104, 1 × 103, 5 × 102, 1 × 102, 5 × 101, 1 × 101, 1 × 100 were mixed respectively with 0.5 g blank soils. The negative control with only blank soil was set. Then the total DNA of the mixture and negative control were extracted by the commercial E.Z.N.A TM Soil DNA Kit (OMEGA, USA) according to the manufacturer’s instructions and was used as template for the PCR.
The PCR products were then loaded onto 1% agarose gels (Sigma–Aldrich, St. Louis, MO, USA). The resulting DNA fragments were visualized by the Gel Doc XR System and analyzed using Quantity One 4.6.3 software (Bio-Rad, Hercules, CA, USA). The size of the amplified PCR products was estimated by comparison with the DL2000 DNA Marker (TaKaRa, Dalian, China).
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4

Rapid Nucleic Acid Detection Protocol

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All nucleic acids used in this study were offered by Sangon Biotech (Shanghai, China) and the sequences are showed in Table S1. Classical swine fever virus (CSFV) and porcine circovirus (PCV) were offered by Chongqing customs technology center. The nucleic acids of pseudorabies virus (PRV) and Peste des petits ruminant virus (PPRV) were gifted by Dr. Ai from Kunming Customs Technology Center. Citric acid and 5-aminosalicylic acid were purchased from Macklin (Shanghai, China). QIAamp DNA Mini Kit was purchased from QIAGEN, Germany. Bst DNA polymerase, 10 × isothermal amplification buffer (20 mM Tris–HCl, 10 mM (NH4)2SO4, 50 mM KCl, 2 mM MgSO4, 0.1% Tween 20, pH = 8.8), and 100 mM MgSO4 were purchased from Eiken Chemical, Japan. DL500 and DL2000 DNA Marker and 2 × Premix Ex Taq (Probe qPCR) were purchased from TaKaRa. ABI 7500 Fast fluorescence quantitative PCR instrument was purchased from life technology TM, USA. Gel imager bought from Bio Rad Co., Ltd. X-ray photoelectron spectroscopy (XPS, XRD-7000) was purchased from JEOL (Japan) for characterizing the elements and their chemical states of CNDs. Transmission electron microscopy (TEM, JEOL Ltd., Japan) was used in morphology characterization. The zeta potential data was obtained by using a Zetasizer nano (Malvern, England).
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5

Phytochemical Analysis and Biomarker Assays

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Rutin, hesperidin, myricetin and quercetin (98% HPLC grade purity) were purchased from Chengdu Alfa Biotechnology Co., Ltd. (Chengdu, China). HPLC grade methanol and glacial acetic acid were obtained from Fuchen (Tianjin) Chemical Reagent Co. Ltd. (Tianjin, China). Anhydrous ethanol (analytical pure AR) were obtained from Tianjin Hengxing Chemical Reagent Manufacturing Co., Ltd. (Tianjin, China).
The assay kits for alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP) and triglyceride (TG) were procured from Shanghai Fuxing Long March Medical Science Co., Ltd. (Shanghai, China). Superoxide dismutase (SOD) and malondialdehyde (MDA), glutathione peroxidase (GSH-PX) and nitric oxide (NO) kits were obtained from Nanjing Jian Cheng Institute of Biological Engineering (Nanjing, China). Tumour necrosis factor-α (TNF-α) and interleukin-6 Enzyme-Linked Immuno Sorbent Assay (ELISA) kits were purchased from Suzhou Calvin Biotechnology Co., Ltd. (Suzhou, China).
Moloney Murine Leukemia Virus (M-MLV) Reverse Transcriptase, SYBR Premix Ex Taq II and DL2000 DNA Marker were supplied by TaKaRa (Dalian, China). Primary antibodies of ACC1 and LPL were purchased from Abcam (Cambridge, Britain). Antibody of GAPDH and HRP-conjugated goat anti rabbit IgG and goat anti mice were procured from Tiandeyue (Beijing) Biotechnology Co., Ltd. (Beijing, China).
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6

HIV-1 Pol Gene Amplification and Sequencing

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Viral RNA was extracted from 140 µL of plasma using a QIAamp Viral RNA Mini Kit (Qiagen, Germany). The amplification of the HIV-1 pol gene fragments (HXB2 2253–3318, covering the full-length protease and the first 240 amino acids of reverse transcriptase codons) was performed using one-step reverse transcription PCR (RT-PCR) by using the PrimeScript one-step RT-PCR Kit Ver. 2 (Takara, China), followed by nested PCR using Ex Taq Hot Start Version DNA Polymerase (Takara, China). The amplified PCR products were electrophoresed on a 1.0% agarose gel with the DL2000 DNA marker (Takara, China). The positive products were purified using the Agarose Gel DNA Extraction Kit (Takara, China), according to the manufacturer’s protocol and sent to Tianyi Huiyuan Genomics Company for Sanger’s sequencing.
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7

Bacterial gDNA Extraction and LAMP Assay

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The genomic DNAs (gDNAs) of bacteria used in the reference assays were extracted by chemical methods using a TIANamp Bacteria DNA Kit (Tiangen Biotech, Beijing, China). The concentrations of the purified gDNAs were calculated using a Nanodrop1000 spectrophotometer (ThermoFisher Scientific, USA) and diluted with water to desired concentrations. The 2 × LAMP mastermix was provided by CapitalBio Corporation (Beijing, China), and bovine serum albumin (BSA, final concentration of 3 mg mL−1) was added to the mastermix (total volume of 60 μL) to decrease the non-specific adsorption of enzymes40 (link). Calcein, manganese chloride, and BSA were purchased from Sigma-Aldrich (Shanghai, China). The DL 2000 DNA marker was purchased from TaKaRa (Dalian, China), and GeneGreen dye was purchased from Tiangen Biotech (Beijing, China). The gel and chip images were obtained and processed using a gel imager (C150, Azure Biosystems, USA). All LAMP primer pairs were synthesized by Invitrogen (Beijing, China), and the sequences are listed in Supplementary Table S1. Each LAMP reaction required four to six primers named F3, B3, FIP, BIP, LF, and LB (LF and LB are not necessary), and the final concentration of each primer in our experiments was 0.3, 0.3, 2.4, 2.4, 1, and 1 μM, respectively.
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8

qRT-PCR Product Analysis by Agarose Gel

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The qRT-PCR products of cDNA and gDNA were investigated using 2% agarose gel electrophoresis with TAE running buffer. DNA was separated by electrophoresis at 100 V for 30 min. The DNA marker was DL2000 DNA Marker (2000-100 bp) (Takara). The bands were examined by UV irradiation.
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9

Apoptosis Pathway Monitoring Protocols

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Monoclonal antibodies against Bcl-2, Bax, P53, P21, Mcl-1, and GAPDH were purchased from Santa Cruz (Santa Cruz, CA, USA). Antibodies against CytC, Fas, FasL, and TRAIL were purchased from Abcam (Cambridge, MA, USA). Mouse anti-γ-H2AX antibody was from Millipore (Billerica, MA, USA). DMEM medium and FBS were purchased from Gibco BRL (Grand Island, NY, USA). FITC annexin V Apopotosis Detection Kit was from BD Biosciences (San Jose, CA, USA). Caspase-Glo 3/7, 8, and 9 assay kits and Plasmid extraction kit were purchased from Promega (Madison, WI, USA). N-acetyl-L-cysteine (NAC) and Reactive Oxygen Species Assay Kit were purchased from Sigma-Aldrich (St. Louis, MO, USA). LipofectamineTM 2000, Dichloro-dihydro-fluorescein diacetate (DCFH-DA), MitoSOXTM Red, MitoTracker Deep Red FM, MitoTracker Green FM and Hoechst 33342 were from Invitrogen (Carlsbad, CA, USA). Trypan Blue Staining Cell Viability Assay Kit was from Beyotime Institute of Biotechnology (Jiangsu, China). Tetramethylrhodamine methyl ester (TMRM) was from Life Technologies (Carlsbad, CA, USA). Z-LEHD-FMK, Z-IETD-FMK, Z-DEVD-FMK were from Calbiochem (San Diego, CA, USA). Colorimetric TUNEL Apoptosis Assay Kit was from Beyotime (Shanghai, China). Mitochondria/Cytosol Fractionation Kit was from BioVision (San Francisco, CA, USA). DL-2000 DNA Marker was from TaKaRa Biotechnology (Dalian, China).
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10

Microbial Culture Media and Antibiotic Discs Procurement

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Normal Nutrient Agar, MacConkey Agar, and Eosin Methylene Blue Agar (EMB) were purchased from Beijing Aoboxing Biotechnology Co., Ltd. (Beijing, China).; DL 2000 DNA Marker was purchased from TAKARA; 2×Taq PCR Mix was purchased from Beijing Yuanchen Technology Co., Ltd. (Beijing, China). Gentamicin (GEN, 10 μg), spectinomycin (SPT, 100 μg), tetracycline (TE, 30 μg), ampicillin (AMP, 10 μg), ceftazidime (TAZ, 30 μg), ofloxacin (FOX, 5 μg), cotrimoxazole (SXT, 1.25/23.75 μg), and other drug-sensitive Discs were purchased from Hangzhou Binhe Microbiological Reagent Co., Ltd. (Hangzhou, China).; amoxicillin/clavulanic acid (AMC, 20/10 μg), florfenicol (FFC, 30 μg), meropenem (MEM, 10 μg), enrofloxacin (ENR, 5 μg), and sulfisoxazole (SIZ, 250/300 μg) were purchased from Hangzhou Microbial Reagent Co., Ltd. (Hangzhou, China).; apramycin (APR, 30 μg), polymyxin (CT, 10 μg), ceftiofur (EFT, 30 μg), and mequindox (SPI, 30 μg) were purchased from Yinuokang Technology Development Co., Ltd. (Tianjin, China). Escherichia coli quality control strain (25922, ATCC, USA) was purchased from Beina Chuanglian Biotechnology Co., Ltd. (Beijing, China).
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