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17 protocols using kod plus kit

1

Plasmid Construction and Lentiviral Transduction

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The plenti6-ratHK2-HA-WT, ratHK2-HA-MTD, ratHK2-HA-SA plasmids were kindly provided by Prof. Nissim Hay (the University of Illinois at Chicago, Chicago, IL 60607, USA). Mutations of HK2 were obtained from PCR-directed mutagenesis using KOD-plus Kit (TOYOBO). shRNAs against target genes were generated with pLKO.1 vector (sequences are shown in Supplementary Table 1). Lentivirus was prepared using a three-plasmid packing system. Briefly, pLKO.1 or plenti6 vectors were co-transfected into 293T cells along with expression vectors containing the VSVG and Δ8.9 genes. Lentivirus was harvested at 24, 48, and 72 h after transfection, and the virus was cleansed by the 0.45-μm filter. Stable cell lines were selected out in 2 μg/mL puromycin or 10 μg/mL blasticidin S for 1 week. Cells were expanded for two passages in drug-free media and frozen for subsequent use. Early passage cells were used for every experiment.
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2

METTL3 and METTL14 Lentiviral Expression

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The human METTL3 cDNA and METTL14 were amplified by KOD-plus Kit (TOYOBO), then subcloned into the vectors pEF5-HA and pCMV-Tag2b, respectively. Mutations and truncations of METTL3 were obtained from PCR-directed mutagenesis. HA-METTL3 was subcloned into the Lentiviral vector pCD513B to yield lentivirus by transfection of HEK-293FT cells. Flag-WTAP plasmid was kindly provided by Dr Jianzhao Liu. The shRNA sequence 5′-GCTAAACCTGAAGAGTGATAT-3′ targeting METTL3 3′-UTR (shMETTL3) was designed and cloned into the Lentiviral vector pLKO.1.
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3

Mouse SRM Promoter Fusion Reporter Constructs

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The DNA fragments of the mouse SRM promoter fusion reporter constructs shown in Fig. 5a were generated from RAW cell genomic DNA by PCR amplification using the KOD-Plus Kit (#KOD-201, Toyobo). The primers used for DNA fragment amplification were as follows: −2,000/+50F: 5′-cAAGCTTtttccagtatcggaatct-3′; −1,000/+50F: 5′-cAAGCTTactcaggacctttggaag-3′; −750/+50 F: 5′-cAAGCTTccttcagctgtgcgttat-3′; −550/+50F: 5′-cAAGCTTttccttgacattttcata-3′; −300/+50F: 5′-cAAGCTTgcccagactagacacgat-3′. The reverse primer for all the fragments was 5′-aCTCGAGcggatggcggcggggcc-3′. The restriction enzymes used for the cloning of fusion reporter constructs included HindIII (5′-AAGCTT-3′) and XhoI (5′-CTCGAG-3′).
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4

Isolation and Sequencing of P35S Promoter

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Primers used for isolating the P35S sequences from different transgenic events were designed using Primer Premier 5.0 software (PREMIER Biosoft International, Palo Alto, CA) according to the nucleotide sequences flanking the P35S promoter. Primers were synthesized by Sangon (Shanghai, China); their sequences are given in Supplementary Table S3 online. The PCR samples were prepared using a KOD-Plus kit (Toyobo, Osaka, Japan) in a sample volume of 50 μL containing 20 ng of genomic DNA, 1× KOD-Plus PCR buffer, 200 μM of each dNTP, 1 mM MgSO4, 100 nM of each primer, and 0.5 units of KOD-Plus DNA polymerase. PCRs were performed on a C1000™ Thermal Cycler (Bio-Rad, Hercules, USA) using the following program: 94°C for 2 min (initial denaturation); 35 cycles of 94°C for 15 s (denaturation) and 68°C for 3 min (annealing and extension); and 68°C for 7 min (final extension). PCR products harboring a target band were recovered and subcloned into the pZErO-2 vector (Invitrogen, Carlsbad, CA, USA) via an EcoRV restriction enzyme site. Ligation products were transformed into Escherichia coli strain TOP10F (Invitrogen, Carlsbad, CA, USA), and positive clones screened. Plasmids containing the PCR products were sequenced using M13 forward and reverse primers (Tsingke, Beijing, China).
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5

Plasmid Cleavage and PCR Analysis

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pUC19 and pBluescript II were linearized by EcoRI digestion, recovered by ethanol precipitation, and treated with 2.5 μM cisplatin or 5-H-Y (DNA base:drug = 30:1) for 24 h or 48 h at 37 °C. After purification using Wizard SV Gel and the PCR Clean-Up System (Promega), 50 ng purified plasmid was used as templates for PCR with the following set of primers: primer F, AGCAAAAACAGGAAGGCAAA and primer R, ACTGGCCGTCGTTTTAC. PCR was performed with the KOD-Plus kit (Toyobo) according to the manufacturer’s protocol. The cycle numbers used were 4, 7, and 10 cycles. The PCR products were electrophoresed on 0.8% agarose gels and stained with EtBr to visualize DNA.
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6

Protein Expression and Purification Protocol

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T4 DNA ligase and Lipo8000 transfection reagent were purchased from Beyotime Biotechnology (Shanghai, China). 2 × Taq Plus Master Mix (Dye Plus) and T4 polynucleotide kinase was purchased from Vazyme Biotechnology (Nanjing, China). The KOD-Plus Mutagenesis Kit and KOD-Plus Kit were from TOYOBO (Osaka, Japan). Ni2+-NTA Superflow resin was purchased from Qiagen Inc. (Hilden, Germany). Dynabeads Protein G, 4,6-diamidino-2-phenylindole (DAPI), MitoTracker, Pierce Silver Stain kit, and Alexa Fluor 488-conjugated secondary antibody were obtained from Thermo Scientific (Waltham, MA, USA). [14C]Thr, [14C]Ser and [14C]Tyr were obtained from Perkin Elmer Inc. (Waltham, MA, USA). PrimeScript RT Master Mix and PrimeSTAR Max DNA Polymerase were obtained from TaKaRa (Kyoto, Japan). Trelief Prestained Protein Ladder and oligonucleotide primers were obtained from Tsingke (Shanghai, China). Competent E. coli BL21(DE3) were purchased from Weidi Biotechnology (Shanghai, China). Serum-free Cell Cryopreservation Medium was obtained from Epizyme Biomedical Technology (Shanghai, China). Anti-c-Myc magnetic beads, kanamycin sulfate and ampicillin sodium were purchased from MedChemExpress (MCE, New Jersey, USA).
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7

Fungal DNA Extraction and Identification

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Small pieces of a colony (3 × 3 mm) grown on malt extract agar (MEA) medium at 25 °C for 10 d were put into 2-mL Cryo tubes. DNA was extracted using the PrepMan™ Ultra Sample Preparation Reagent (Applied Biosystems, Foster City, CA, USA). PCR was performed using a KOD-Plus Kit (Toyobo, Osaka, Japan) following the manufacturer’s protocol. The rDNA large subunit region (LSU D1/D2) was amplified with the primer pair NL1/NL4 (O’donnell, 1993 ). To amplify the ITS region, the primers ITS1 and ITS4 were used (White, Bruns, Lee, & Taylor, 1990 ). Amplification of the DNA fragments was performed using the GeneAmp PCR System 9700 (Applied Biosystems). PCR products were checked by agarose gel electrophoresis and purified using an AMPureKit (Agencourt Biosciences, Beverly, MA, USA). Sequencing reactions were performed by using the Big Dye Terminator V3.1 Cycle Sequencing Kit (Applied Biosystems) and the same PCR primers. The newly generated sequence data were deposited in the DNA Data Bank of Japan (DDBJ) under the accession numbers provided in Table 1.
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8

Targeted RNAi silencing in tomato

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The RNAi construct was designed using Gateway technology (Invitrogen). Total RNA was extracted from WT ovaries using the RNeasy Plant Mini Kit (QIAGEN), followed by the removal of genomic DNA using RNA Clean & Concentrator (ZYMO RESEARCH). cDNAs were then synthesized using the SuperScript VILO cDNA Synthesis Kit (Thermo Fisher Scientific). A 521 bp fragment of the Solyc04g077010 transcript was amplified using the KOD Plus kit (TOYOBO); the cDNA was used as the template, and SlXIPRNAiF1 and SlXIPRNAiR1 were the primers (Supplementary Table S2). The amplicon was then cloned into the donor pBI-sense, antisense-GW vector (INPLANTA INNOVATIONS INC., Japan), allowing expression under the control of the constitutive 35S promoter. The resulting plasmid was introduced into WT Micro-Tom by Agrobacterium-mediated transformation using A. tumefaciens GV2260 (Sun et al., 2006 (link)). Transgenic lines were selected on Murashige and Skoog (MS) agar plates containing kanamycin (100 mg L-1).
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9

Extraction and Analysis of ADAM10 mRNA from Mouse Brain

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Total RNA from adult C57/BL6 mice brains was prepared using the TRIzol reagent, according to the manufacturer's protocol (cat. no. 15596-026, Invitrogen; Thermo Fisher Scientific, Inc., Waltham, MA, USA) and a glass homogenizer, this was incubated subsequently with DNase I for 1 h at 37°C to remove any contaminating DNA. RNA was reverse transcribed to cDNA using a M-MLV RTase cDNA Synthesis kit (cat. no. D6130, Takara Bio, Inc., Otsu, Japan) according to the manufacturer's protocol. The polymerase chain reaction (PCR) amplification of ADAM10 cDNA was performed using the KOD-Plus kit (Toyobo Co., Ltd., Osaka, Japan) and the following primers, sense, 5′GGTGAAACGCATAAGAATC-3′ and antisense, 5′CACTGAACTGCTTGCTCC-3′ under conditions as follows: Denaturation at 94°C for 4 min; 35 cycles of denaturation at 94°C for 30 sec, annealing at 56°C for 40 sec, and extension at 68°C for 90 sec; and extension at 68°C for 5 min. The amplified PCR fragments were analyzed on agarose gels. The identity of the PCR products was confirmed with restriction analysis. For restriction reactions, the electrophoresed PCR products were purified from agarose gels using QIAquick Gel Extraction kit (Qiagen GmbH, Hilden, Germany) and cloned into pGEM-T Easy plasmid (Promega Corporation, Madison, WI, USA) following the manufacturer's protocol.
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10

PCR Amplification of Genetic Deletions

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PCR amplification was performed using DNA from the patient and the first-degree relatives with a set of primers across the deletion. Additionally, semi-quantitative PCR was performed with a set of primers within the deleted region and those outside the deletion (KOD-Plus kit, TOYOBO, Osaka, Japan). The primer sequences are shown in Supplementary Table S3.
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