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7 protocols using pmd19 t easy vector

1

Transient Expression of GFP-IgBBX in Tobacco

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The p35S::GFP-IgBBX constructs were introduced into tobacco epidermal cells via the Agrobacterium-infiltrated tobacco (Nicotiana benthamiana) leaf method [26 (link)]. The plasmid of IgBBX for transient transformation was generated using the Invitrogen Gateway system, according to the manufacturer’s instructions. The IgBBX ORFs, lacking the stop codon, were amplified using a Phusion®High-Fidelity PCR kit (New England Biolabs, Ipswich, MA, USA) (primers listed in Table S1), then inserted into the pMD19-T easy vector (TaKaRa, Tokyo, Japan) to allow its sequencing-based validation. Each pENTRTM1A-IgBBX plasmid was previously subjected to the LR Clonase™ II enzyme mix (Invitrogen, Carlsbad, CA, USA) reaction to obtain GFP-fused constructs using the binary vector pMDC43, resulting in the plasmid p35S::GFP-IgBBX. For transient expression, Agrobacterium tumefaciens strain EHA105 carrying the pMDC43 and pMDC43-IgBBX was grown separately to OD600 = 0.8 and coinfiltrated with the p19 strain into leaves of five-week-old N. benthamiana. The YFP fluorescent signals were monitored 48 to 72 h after infiltration using a confocal laser scanning microscopy (LSM 700, Carl Zeiss).
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2

Tick Hemolymph EV Marker Identification

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In this study, we used an experimental approach combining sequence alignment based on tick hemolymph EV proteomics and previous R. haemaphysaloides transcriptome data with sequence search for the identification of tick hemolymph EV markers. The Rh14-3-3ζ, Rh14-3-3ε, RhCD9, RhTSG101, RhFerritin-1, RhFerritin-2, RhCytochrome c and RhCalnexin sequences were found in the salivary gland and midgut transcriptomes of fed R. haemaphysaloides. Complementary DNAs (cDNAs) were synthesized by HiScript III RT SuperMix (Vazyme, Nanjing, China) from the total RNA of the R. haemaphysaloides salivary gland and midgut. Gene-specific oligonucleotide primers for PCR are listed in Additional file 5: Table S1. The sequences were routinely cloned into the pMD-19 T easy vector (Takara, Dalian, China) using PrimeSTAR Max Premix (Takara), and the obtained clones were sequenced.
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3

Salmonella Primary Transcriptome Profiling

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The full-length cDNAs of the Salmonella primary Sal-1 were obtained using the SMARTerTM RACE cDNA amplification kit (Clontech, Mountain View, CA) according to the manufacturer’s instructions. Because the RNA template was from a prokaryotic organism and lacked a polyadenylated tail, we thus added a poly(A) tail using Poly(A) Polymerase (Takara). Then, the first-strand cDNA was synthesised using a modified oligo(dT) primer (5′-RACE CDS primer A or 3′-RACE CDS primer A), and the SMARTerTM II A oligonucleotide was added for 5′-RACE cDNA synthesis. The gene-specific antisense primer sal-GSP1 was used for 5′-RACE amplification, and sal-GSP2 was used for 3′-RACE amplification. The cDNA was amplified using the Advantage 2 PCR kit (Clontech) with the above gene-specific primers and the Universal Primer A Mix in the SMARTerTM RACE kit. The RACE product was electrophoresed, purified, and ligated into the pMD19-T Easy vector (Takara). The ligations were transformed into E. coli Top 10 chemically competent cells. The plasmids were extracted from bacterial cell suspensions using the E.Z.N.A.® Plasmid Mini Kit (Omega Bio-Tek, Norcross, GA) for sequence analysis.
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4

PCR Amplification and Sequencing Protocol

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Polymerase chain reaction amplification of a 1,347 bp region surrounding the target sequence was performed on selected co-transformed DNA samples using the primers listed in Supplementary Table S2. PCR was performed using T5 direct PCR kit (plant) (Tsingke biotech, Beijing, China) in a thermal cycler with the following program: 95°C for 5 min, 30 cycles of 95°C for 30 s, 55°C for 30 s, 72°C for 1.5 min, and 72°C for 10 min. The PCR products were then run on a 1% agarose gel, and the target bands were extracted using the Omega Gel Extraction Kit (Omega Bio-tek, GA, United States). Target gel extraction products (∼1,000 ng) were digested with 5 u MwoI restriction enzyme at 60°C for 40 min. Digested DNA was then run on a 1% agarose gel in 1 × TBE for 20 min at 180 V, then imaged on a UV gel imager (Bio-Rad Laboratories, Shanghai, China). Gel bands that appeared to be undigested were then extracted using the Omega Gel Extraction Kit (Omega Bio-tek, GA, United States). And cloned into the pMD19-T easy vector (TaKaRa, Toyoto, Japan). Five to twenty clones for each line were sequenced.
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5

Cloning of Polyphenol Oxidase Genes

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The cDNA fragments were obtained from the previous transcriptome of Longjing 43. The 5′ and 3′ sequences of CsPPO1 and CsPPO2 were acquired by rapid amplification of RACE-PCR using the manufacturer’s protocol (SMARTer® RACE 5′/3′Kit, Clontech Lab, Inc., Mountain View, CA, USA). The PCR products were ligated into a pMD-19T easy vector (Takara, Dalian, China) after purification. After the 3′ and 5′ sequences were obtained, the full-length cDNA sequences of CsPPO1 and CsPPO2 were cloned by RT-PCR reaction using primers PPO1-full1, PPO1-full2, PPO2-full1, and PPO2-full2. All the primers used in RACE are listed in Table 2.
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6

Cloning and Sequencing of CmMYB2 from Jinba

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A 1 μg aliquot of RNA extracted from the leaves of a Jinba plant using RNAiso reagent (TaKaRa, Tokyo, Japan) was converted into ss cDNA using M-MLV reverse transcriptase (TaKaRa). The full-length CmMYB2 sequence of Jinba was inferred from the version of the sequence present in the variety Zhongshanzigui22 (link). The full-length CmMYB2 cDNA sequence was subsequently inserted into a pMD19-T easy vector (TaKaRa) for validation by sequencing. The relevant primers used for this procedure are listed in Table S1.
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7

Gel Extraction and Amplification Protocol

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Selected bands were excised from the gel with a sterile scalpel, washed with deionized water and incubated in 35 μL TE buffer at 4°C overnight. The extracted gel mix was heated at 90°C for 10 min, and 4 μL of the solution served as the template for PCR re-amplifying by using the same set of primers and programs described previously but without GC clamp. PCR products were electrophoresed on a 2% agarose gel, purified and then cloned into the PMD19-T Easy vector (TaKaRa), transformed into competent Escherichia coli Nova blue cells, and screened for positive plasmid insertions according to the manufacturer protocol. Plasmid DNA was extracted from positive clones, amplified by PCR and sent for sequencing (TaKaRa).
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