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Sybr premix ex taqtm 2 tli rnaseh plus

Manufactured by Takara Bio
Sourced in Japan, China, United States, Canada, Germany

SYBR® Premix Ex TaqTM II (Tli RNaseH Plus) is a ready-to-use PCR master mix that contains SYBR® Green I dye, Tli RNase H Plus, and optimized buffer components. It is designed for real-time PCR amplification and detection of target DNA sequences.

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158 protocols using sybr premix ex taqtm 2 tli rnaseh plus

1

Reverse Transcription and Real-Time PCR Protocol

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Total RNA was primed with 1 μl oligo dT (12–18) primer (50 μM) in a 6‐μl reaction system, and then incubated at 70°C for 10 min and rapidly cooled on ice prior to reverse transcription reaction. Reverse transcription was carried out at 42°C for 1 h in a final volume of 10 μl containing 2 μl of 5× M‐MLV buffer (TAKARA BIO), 0.5 μl of 10 mM dNTP mix (NEW ENGLAND Biolabs), 0.25 μl of RNase Inhibitor (TAKARA BIO), 1 μl of RTase M‐MLV (RNase H‐) (TAKARA BIO) followed by incubation at 70°C for 15 min to terminate the reaction and stored at ‐20°C until use. For real‐time PCR, the cDNA samples were diluted tenfold.
RT‐qPCR was conducted on LightCycler 96 (Roche). Each reaction mixture consisted of 2 μl of cDNA, 0.5 μl each of forward (10 μM) and reverse primers (10 μM), 12.5 μl 2× SYBR Premix Ex TaqTM II (Tli RNaseH Plus) (TAKARA BIO), and 9.5 μl of nuclease‐free water (Millipore) in a total reaction volume of 25 μl. The thermal cycler program consisted of 40 cycles of 95°C for 15 s and 60°C for 1 min. Primers were designed using Primer Premier 5.0 (PRIMIER Biosoft). The primer sequences are listed in Table S1. Data were obtained from three replicate assays for each sample with normalization to ActB, and relative gene abundance was calculated using the method of 2−ΔΔCt as previously described.10
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2

Validating RNA-seq Gene Expression Data

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We randomly selected 8 genes (including four upregulated genes and four downregulated genes) for real-time PCR in 1.85Trp and 6.35Trp groups to confirm the reproducibility and accuracy of the RNA-seq gene expression data. Using an RNAiso Plus kit (Takara, Kyoto, Japan), total RNA was isolated from intestinal tract tissues of fishes. After checking the RNA quality, as described in the RNA extraction section, reverse transcription was performed using the PrimeScript™ RT Reagent Kit with gDNA Eraser (Takara, Kyoto, Japan) according to the manufacturer's protocol. Real-time PCR experiments were performed using a LightCycler® 96 Real-Time PCR system (Roche Applied Science) in a 25 μL reaction volume containing 12.5 μL of 2 × SYBR® Premix Ex TaqTM II (Tli RNaseH Plus; Takara, Kyoto, Japan), 1.25 μL each of the forward and reverse primers (10 μM), 8 μL of deionized water, and 2 μL (~100 ng) of cDNA. The β-actin gene was used as the reference gene, and the primers of eight genes were designed using Primer. The thermal cycling conditions were 3 min at 95°C, followed by 37 reaction cycles (95°C for 30 s, 60°C for 30 s, and 72°C for 30 s), and an extension for 10 min at 72°C. We calculated the relative gene expression levels with the comparative CT method (referred to as the 2−ΔΔCT method) (29 (link)), with three replicates for each reaction.
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3

Quantifying Fungal Biomass in Infected Apples

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qPCR assays with DNA samples extracted from infected apples were performed to determine fungal biomass using SYBR Premix Ex Taq TM II (Tli RNaseH Plus) (TAKARA, Japan) with the Bio-Rad CFX96 (Bio-Rad, Hercules, CA, United States) and the primer pair patF_F and/patF_R. Two negative controls were also performed (one without primers and fungal DNA and the other one without fungal DNA) to rule out any possible matrix effect. The PCR conditions were as follows: 94°C for 30 s, 40 cycles of 94°C for 20 s, 60°C for 20 s, and 72°C for 20 s. The dissociation curve analysis followed the same trend as the amplification cycle and was constructed by continuously measuring the fluorescence when increasing the temperature from 65 to 95°C, at the rate of 0.5°C/s. The threshold cycle (CT) values were automatically determined by the CFX ManagerTM software (Bio-Rad Laboratories). For each DNA sample, three technical replicates were analyzed. Fungal biomass was expressed as ng DNA/μg decayed apple tissue.
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4

FMDV Vaccine Strain Propagation and Characterization

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Baby Hamster Syrian Kidney (BHK-21cells) were cultured in Dulbeccoʼs modified Eagleʼs medium (DMEM) supplemented with 10% FBS. FMDV strains, O/MYA98/BY/2010 and Asia1/JSL/ZK/06 investigated extensively as vaccine strains, were provided by Zhongnongweite biotechnology Co., Ltd. Each strain was propagated in BHK-21 cells at a multiplicity of infection of 0.001 and incubated in 5% CO2 at 37 °C. A PrimeScriptTM RT reagent kit containing gDNA Eraser and SYBR Premix Ex TaqTM II (Tli RNaseH Plus) was purchased from TaKaRa (Dalian, China). MTS assay was available from Abcam (Cambridge, UK). The 50% tissue culture infectious dose (TCID50) was measured with the Reed and Muench method. Trehalose, CuSO4·5H2O were purchased from sigma (MO, USA). All other chemicals were analytical grade reagents purchased from Beijing Chemical works (Beijing, China) and all solutions were prepared using Milli-Q grade water (Millipore,USA).
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5

qRT-PCR Analysis of EspP2-Treated PK15 Cells

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Refer to the previous procedure for qRT-PCR [48 (link)]. RNA from PK15 cells incubated with EspP2 was isolated using a UNIQ-10 Column Total RNA Purification Kit (Sangon, China). Two-step RT-PCR was performed using PrimeScriptTM RT Reagent Kit with gDNA Eraser (Takara, Japan). Utilizing SYBR Premix EX TaqTM II (Tli RNaseH Plus; Takara, Japan), transcripts were subjected to qRT-PCR analysis. Gene expression was quantified using the 2[-ΔΔC(T)] method, and results are presented relative to expression of β-actin. The Lightcycler96 (Roche, Basel, Switzerland) system was used for the qPCR. For each sample, there were three biological replicates and the qRT-PCR assay was repeated three times.
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6

Quantitative RT-PCR Analysis of Inflammatory Cytokines

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According to the manufacturer’s instructions, total RNA from cell cultures was extracted using TRIzol reagent (Invitrogen). The cDNA was then synthesized from total RNA using the PrimeScript RT reagent kit with the gDNA Eraser (Takara, Shiga, Japan) method. Real-time qPCR was performed using an Applied Biosystems 7500 Real-Time PCR Systems (Thermo Fisher Scientific, Waltham, MA, USA) using the SYBR Premix EX TaqTM II (Tli RNaseH Plus; Takara). The 18S was treated as an internal control. Data were analyzed using the Applied Biosystems 7500 software program, version 2.3 (Applied Biosystems, Foster City, CA, USA) with the automatic Ct setting for adapting baseline and a threshold for Ct determinations. The relative expression levels of mRNA were calculated by the comparative cycle threshold (Ct) and 2−ΔΔCT method.
The sequences of the primers used were the following:
IL6-forward: 5ʹ-TCTCCACAAGCGCCTTCG-3ʹ;
IL6-reverse: 5ʹ-CTCAGGGCTGAGATGCCG-3ʹ;
IL8-forward: 5ʹ-CACCACTTTCTGGAGCAT-3ʹ;
IL8-reverse: 5ʹ-CATTGAGGAATAGGAGGG-3ʹ;
IL11-forward: 5ʹ-TCTCTCCTGGCGGACACG-3ʹ;
IL11-reverse: 5ʹ-AATCCAGGTTGTGGTCCCC-3ʹ;
18S-forward: 5ʹ-CCCGGGGAGGTAGTGACGAAAAAT-3ʹ;
18S-reverse: 5ʹ-CGCCCGCCCGCTCCCAAGAT-3ʹ.
The reaction was performed for 30 s at 95°C, followed by 45 cycles at 95°C for 5 s, 59°C for 34 s, 72°C for 30 s, with a final extension at 72°C for 30 s. Each reaction was performed in triplicate.
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7

Molecular Toolkit for Citrus Genetic Studies

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Primer STARTM HS DNA Polymerase, Taq DNA Polymerase, T4 DNA Ligase, a Star Prep Plasmid Miniprep Kit, a Universal DNA Purification Kit, a DNA Fragment Purification Kit, PrimeScriptTM RT Master Mix (for Real Time PCR) and SYBR® Premix Ex TaqTM II (Tli RNaseH Plus), as well as restriction enzymes SpeI, BamHI, HindIII, EcoRI, and D2000 DNA Ladder Marker, were purchased from TaKaRa Bio. A SV Total RNA Isolation System was purchased from Promega. All primer synthesis and sequencing was performed by Invitrogen. Primer sequences are shown in Supplementary Table S1. Susceptible cultivars of Citrus reticulata, commonly known as Xinhuigan and Orah were maintained in a greenhouse.
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8

Quantitative Real-Time PCR Protocol

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Total RNA was extracted from tissues and cells using the RNAiso Plus reagent (TaKaRa, Tokyo, Japan) according to the manufacturer’s instructions. RNA concentration was detected using a NanoDropTM 2000 spectrophotometer (Thermo Scientific, Waltham, MA, United States). Complementary DNA (cDNA) was synthesized using the PrimeScriptTM RT reagent kit with gDNA Eraser (TaKaRa). cDNA was examined by qRT-PCR using the SYBR®Premix Ex TaqTM II (Tli RNaseH Plus) (TaKaRa) with specific primers and the CFX384 Real-Time PCR Detection System (Bio-Rad, Hercules, CA, United States). Data were normalized by GADPH and β-actin mRNA expression for each sample. The relative expression of mRNAs was calculated using the comparative 2-ΔΔCT method. Primer sequences used in this study are shown in Supplementary Table S1; all primers used in this study were synthesized by Tsingke (Chengdu, China).
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9

Quantification of Cell Division Cycle Genes

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Total RNA was extracted by using Trizol (Invitrogen) according to the manufacturer's instructions. 500 ng of total RNA was reverse transcribed to cDNA using PrimeScriptTM Ⅱ 1st strand cDNA Synthesis Kit (Takara). RT-qPCR was performed with SYBR® Premix Ex TaqTM II (Tli RNaseH Plus) (Takara) on 7500 Real-Time PCR Systems (Applied Biosystems, USA). Gene expression level was determined by using the ΔΔcycle threshold method normalized to β-Actin. qPCR primers used were as follows: CDCA2 (forward primer ATGACCGGCTGTCTGGAAT and reverse primer GCTGAGACCTTCCTTTCTGGT), CDCA3 (forward GGACCCTGAGACTCCCAGAT and reverse GCCGCTTACCCTGTCGTAG), CDCA4 (forward ATTTGAAACGCTGGAGACT and reverse CCCATCATGCCTGTCAGTA), CDCA5 (forward AGAAAGTCAGGCGTTCCTACAG and reverse GGGAGATTCCAGGGAGAGTCAT), CDCA7 (forward TACAGCCTTCCCGAACTGAC and reverse TAACGAACTGGCCGGTATTT), CDCA8 (forward TTGACTACTTCGCCCTTG and reverse CTTCTTCTTCCTCTTCCACTA) and Actin (forward ACTCTTCCAGCCTTCCTTCC and reverse AGCACTGTGTTGGCGTACAG).
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10

Quantitative RT-PCR Analysis of HCC Samples

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Total RNA was isolated from HCC tissues and HCC cells using TRIZOL® reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. The first strand cDNA was synthesized using the Revertid™ First Strand cDNA Synthesis Kit (Fermentas, Burlington, ON, Canada). cDNA (2 μL) obtained from each sample was amplified and quantified by real-time PCR using SYBR® Premix Ex TaqTM II (Tli RNaseH Plus, Takara, Shiga, Japan). The human GAPDH gene served as an internal control gene to ensure that an equal amount of mRNA was analyzed from each sample. The primers were synthesized by GenePharma Co., Ltd. (Shanghai, China) and the sequences are shown in Table 3. Relative gene expression was calculated with the 2−ΔΔCt method. Three independent experimental replicates were performed.
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