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Sybr premix ex taq 1

Manufactured by Takara Bio
Sourced in Japan

SYBR Premix Ex Taq I is a ready-to-use PCR master mix that contains SYBR Green I dye, a DNA-binding fluorescent dye, and a chemically-modified hot-start Taq DNA polymerase. It is designed for real-time quantitative PCR (qPCR) applications.

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15 protocols using sybr premix ex taq 1

1

Quantitative Real-Time PCR Analysis of Microglia

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Total RNA was isolated from treated-microglial cells by using Trizol reagent (Invitrogen Life Technologies, California, USA). The quality and quantity of total RNA were measured by NanoDrop 2000 spectrophotometer (NanoDrop Technologies, Thermo Scientific, USA). According to the manufacturer's instructions, 1 μg total RNA was reverse-transcribed and synthesized the complementary DNA by using PrimeScriptTM RT Master Mix (TaKaRa, Japan). Real-time qPCR was carried out using SYBR® Premix Ex Taq I (TaKaRa, Japan) following the instructions of reagent kit on a Quant Studio 5 Real-Time PCR System (Applied Biosystems, USA). The primer sequences of target genes were shown in Table 1. GAPDH was regarded as the internal standard to normalize other target genes, and the 2(–ΔΔct) method was used to analyzed the relative expression of the target genes. Each sample was run in triplicate, and each experiment was repeated at least thrice.
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2

Gene Expression Analysis Protocol

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Transfection was conducted with Lipofectamine 2000 (Invitrogen) following the protocol of the manufacturer. Generally, 5 × 105 cells were seeded into 6-well plates one day before transfection. When cells reached the 80% confluence, the plasmid DNA and Lipofectamine 2000 were diluted with the Opti-MEM I Reduced Serum Medium, respectively, and then mixed together. After incubating for 20 minutes at room temperature, the mixture was added into the plate drop by drop. After 24–48 h, the cells were used for further experiments.
TRIzol reagent (Invitrogen, Carlsbad, CA, USA) was used to extract RNA from 5 × 105 cells following the protocol of the manufacturer. Total RNA was finally suspended in 20 µL of RNase-free water. The purity and quality of the isolated RNA was evaluated by NanoDrop with A260/A280 ratio of 1.9–2.0. A total of 500 ng RNA was used to synthesize cDNAs using the PrimeScript reverse transcriptase reagent kit (TaKaRa, Shiga, Japan), according to the protocol of the manufacturer. qRT-PCR was performed with the Roche Light Cycler 480 II using the SYBR Premix Ex Taq I (TaKaRa, Japan). Each reaction contained 2 μL of cDNA in a total volume of 20 μL. Relative RNA abundances were calculated by the standard 2-ΔΔCt method after normalization to GAPDH. The specific primers used in the article are provided in Supplementary Table 1.
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3

WIF1 Regulation in Cell Proliferation

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The following were used in the study: Dulbecco’s modified Eagle’s medium (DMEM), lipofectamine 2000, pmirGLO plasmid, Fetal bovine serum (FBS), pcDNA3.1 plasmid and Trizol reagent (Invitrogen, Carlsbad, US); matrigel (BD, New Jersey, US); SurePrep™ Nuclear or Cytoplasmic RNA Purification Kit, PrimeScrip™ RT Master Mix, SYBR Premix Ex Taq I and PrimeScript miRNA cDNA Synthesis Kit (TaKaRa, Shiga, Japan); protease inhibitor cocktail (Sigma, St. Louis, US); Dual-Luciferase Reporter Assay System (Promega, Madison, US); CCK-8 test kit (Dojindo Corp, Kyushu, Japan); antibodies against WIF1(#5652), Ki-67(#9449) and β-Actin (#4967) (Cell Signaling Technology, Danvers, US).
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4

RNA Extraction and qRT-PCR Protocol

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Twenty-four hours after transfection, total RNA was extracted from the cells using TRIzol reagent (Invitrogen, Carlsbad, CA) and was then reverse transcribed to complementary DNA (cDNA). The primers (sequences shown in Supplementary Table S2) were synthesized by Sangon Biotech (Shanghai, China). SYBR premix EX Taq I (Takara, Japan) was used as a DNA-specific fluorescent dye, and the results were analysed by a 7500 real-time PCR system (Applied Biosystems, Foster City, CA) through the comparative Ct (ΔCt) method. The experiments were repeated three times, and all three technical replicates were included for each data point.
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5

Quantitative Gene Expression Analysis in Canine Cells

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Total RNA was extracted with RiboEx reagent (GeneAll, South Korea) and purified with a Hybrid-R kit (GeneAll, South Korea) as directed by the manufacturer. A RevertAid First-Strand cDNA Synthesis kit mRNA (Thermo Fisher Scientific, USA) was used to synthesize cDNA from 500 ng of mRNA. SYBR Premix Ex Taq I™ (Takara Bio, Japan) was used for PCR on a CFX96 real-time PCR Detection System (Bio-Rad, South Korea). Results of quantitative reverse transcription-PCR (qRT-PCR) were evaluated as Ct values and quantified using the 2−ΔΔCt method. GAPDH was used as a reference gene to analyze the canine’s gene quantitatively. Primer sequences used for qRT-PCR amplification were as follows: ACTA2 (a-SMA) F: 5’-CATCACCAACTGGGACGACA-3’, R: 5’-GTACATGGCTGGGACGTTGA-3’; VIM (Vimentin) F: 5’-GCGGGAGAAGATGTTGACAATG-3’, R: 5’-CGCAGCCACGCTTTCATATT-3’; GAPDH F: 5’-ATGGTGAAGGTCGGAGTCAA-3’, R: 5’-ATCACCCCATTTGATGTTGG-3’; CDH1 (E-cadherin1) F: 5’-AAATCACATCCTACACCGCC-3’, R: 5’-ATTAACCTCCAGCCAACCG-3’.
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6

Quantitative PCR Analysis of Autophagy Genes

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Trizol reagent (Invitrogen, USA) was used to extract the total RNA of different experimental groups for reverse transcription (the reverse transcription kit was purchased from Takara, Japan). SYBR Premix Ex Taq I (Takara, Japan) was then used for real-time quantitative PCR (the instrument was purchased from Bio-Rad, USA) to detect the expression levels of Pink1, Beclin1, Parkin, P62, and ATG5. Each experiment was repeated 3 times for calibration with Actin as the internal reference. The PCR primers sequence used in this study are shown in Table 1.
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7

Quantitative Analysis of Gene Expression in Microglia

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Total RNA was isolated from treated-microglial cells by using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA). The quality and quantity of total RNA were measured by Nano Drop 2000 spectrophotometer (Nano Drop Technologies, Thermo Scientific, Waltham, MA, USA). According to the manufacturer’s instructions, 1 µg total RNA was reverse-transcribed and synthesized the complementary DNA by using Prime Script TM RT Master Mix (TaKaRa, Tokyo, Japan). Real-time qPCR was carried out using SYBR® Premix Ex Taq I (TaKaRa, Japan) following the instructions of reagent kit on a Quant Studio 5 Real-Time PCR System (Applied Biosystems, Waltham, MA, USA). The primer sequences of target genes were shown in Table 1. β-actin was regarded as the internal standard to normalize other target genes, and the 2(−ΔΔct) method was used to analyze the relative expression of the target genes. Each sample was run in triplicate, and each experiment was repeated at least thrice.
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8

Investigating Stem Cell Transcriptional Profiles

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Forty-eight hours after treatment with TiO2 NPs in concentration around their IC50 (100 and 200 µg/ml for rBMSCs and rATSCs, respectively), total RNA was extracted from rBMSCs and rATSCs using an RNA extract kit (Bio Basic INC, USA). cDNA was synthesized using the PrimeScriptTM RT Kit (TaKaRa, Japan) and used for real-time PCR using SYBR® Premix Ex Taq™ I (TaKaRa, Japan) and a pair of specific primers for Nanog, P53, SIRT1, NFkb, RUNX2, Osteocalcin, OCT4, and SOX2 genes (Table 1). The real-time PCR reaction was performed in a thermal cycler (BioRad, USA). After initial denaturation at 95 °C for 3 min, amplification was carried out in 40 cycles at 95 °C for 20 s, 60 °C for 20 s, and 72 °C for the 30 s. Relative expression of the genes in each source of the cells was calculated related to the GAPDH housekeeping gene.

Primer sequences of each gene

GenePrimer nameSequenceLength
NanogForwardGAGACTGCCTCTCCTCCGCCTT22
ReverseGTGCACACAACTGGGCCTGA20
P53ForwardGTCGGCTCCGACTATACCACTATC24
ReverseCTCTCTTTGCACTCCCTGGGG21
GAPDHForwardTCAAGAAGGTGGTGAAGCAG20
ReverseAGGTGGAAGAATGGGAGTTG20
NF-KBForwardGTCGGCTCCGACTATACCACT21
ReverseTCCTCTCTTTGCACTCCCTGGG22
Sirt 1ForwardCGCCTTATCCTCTAGTTCCTGTG23
ReverseCGGTCTGTCAGCATCATCTTCC22
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9

Quantitative Analysis of KNTC1 Expression

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According to the manufacturer’s instructions, we used TRIzol (Invitrogen) to extract total cell RNA, PrimeScript™ RT Master Mix (RR036A, TaKaRa) kit for reverse transcription, and SYBR® Premix Ex Taq™ I (RR820A, TaKaRa) reagent to perform qPCR on the BioRad CFX96 system. The primers were synthesized by Sangon Biotech (Shanghai, China) and their sequences were as follows: KNTC1, forward 5-TCCCATCGCAGGACGAAAAA-3′ and reverse 5′-ATGTGCTGGCTTTCCGATCA −3′; GAPDH, forward 5′- CCCCACCACACTGAATCTCC −3′ and reverse 5′- GTACATGACAAGGTGCGGCT-3′.
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10

Total RNA extraction and qRT-PCR analysis

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Total RNA was extracted from the cells using the Trizol reagent (Invitrogen, Carlsbad, CA), and then reverse transcribed into cDNA. The PCR primers were synthesized by Sangon Biotech (Shanghai, China). Primer sequences are shown in Supplementary Table S1. Reactions were performed using SYBR premix EX Taq I (Takara, Japan) and analyzed by the CFX Connect™ Real-Time PCR Detection System (Bio-Rad, USA). Relative mRNA levels were calculated using the comparative Ct (ΔCt) method. Experiments were repeated three times and three technical replicates were included for each data point.
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