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9 protocols using tb green premix ex tag 2

1

Quantification of CES2 Expression

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Total RNA was extracted from the cultured cells using RNAiso Plus (TaKaRa). Reverse transcription was performed using the PrimeScript RT reagent kit with gDNA Eraser (TaKaRa). RT-qPCR was performed using TB Green Premix EX Tag II (TaKaRa), according to the manufacturer’s instructions. Primers were as follows: GAPDH, forward (F): 5’-ACGAGTGTGTCTTCGCTTGT-3’, reverse (R): 5’-TCTTTACTCTTGCCCCGCAG-3’; CES2, forward (F): 5’-GCACCGTCAAGGCTGAGAAC-3’, reverse (R): 5’-TGGTGAAGACGCCAGTGGA-3’.
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2

Quantitative Analysis of RNA Expression

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Total RNA was isolated from RAW 264.7 cells and HT-29 cells by using TRIzol reagent (Invitrogen, Carlsbad, California, USA). The concentration of total RNA was measured using NanoDrop spectrometer (ND-2000, Thermo Scientific, USA). qRT-PCR was performed on CFX96 Real-Time PCR Detection System (Bio-Rad, Hercules, California, USA) using TB Green Premix Ex Tag II (TaKaRa Bio Inc., Japan) with 25 μL reaction mixtures (primers are enlisted in Table S1). PCR program was reacted with amplification with 39 cycles at 95°C for 30 s, at 95°C for 5 s, and at 60°C for 30s. The relative mRNA levels were quantified by the 2−ΔΔCt method and all data were normalized to GAPDH (the internal control). The sequences of all primers involving in this study were listed in Table S1.
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3

RNA Isolation and qRT-PCR Protocol

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First, 1 mL TRIzol (TaKaRa, Shiga, Japan; cat. no. 9109) was added to each well of a six-well plate containing treated cells. RNA was then isolated and purified according to the manufacturer’s instructions. A Nanophotometer 50 instrument was used to measure RNA concentrations and purity, and the A260/A280 values of all samples were between 1.8 and 2.0, indicating high RNA quality. Prime Script RT Master Mix (TaKaRa; cat. no. RR036A) was used for reverse transcription, and TB Green Premix Ex Tag II (TaKaRa; cat. no. RR820A) was used for amplification on a 7500 Real-Time PCR System (Applied Biosystems, Foster City, CA, USA). Thermocycling conditions were as follows: 95 °C for 30 s, followed by 40 cycles at 95 °C for 5 s and 60 °C for 35 s. The obtained Ct values were normalized using the 2−ΔΔCt formula, with GAPDH as the housekeeping gene. The primer sequences are detailed in Supplementary Fig. S2.
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4

Quantitative RT-PCR Analysis of Gene Expression

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Second passage cells were treated with inhibitors until they reached 80% confluence. At the end of experiments, cells were washed with PBS and treated with TRIzol (TaKaRa; Cat. No. 9109), and RNA was extracted according to the manufacturer’s protocol. The NanoVne instrument (GE Healthcare) was used to measure the purity. Samples with A260/280 values between 1.8 and 2.0 were used for subsequent experiments. The Prime Script RT Master Mix (TaKaRa; Cat. No. RR036A) was used for reverse transcription, and TB Green Premix Ex Tag II (TaKaRa; Cat. No. RR820A) was used for amplification on a 7500 Real-Time PCR System (Applied Biosystems, Foster City, CA, United States). Thermocycling conditions were as follows: 95°C for 30 s, followed by 40 cycles at 95°C for 5 s and 60°C for 35 s. The obtained Ct values were normalized using the 2–ΔΔCt formula, with GAPDH as the housekeeping gene. The primer sequences are listed in the Supplementary Figure 2.
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5

Quantitative Gene Expression Analysis in Poplar

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Total RNA was extracted from poplars with a Plant RNA Extraction Kit TRIzol® Reagent (Invitrogen, America, 15 596‐026), and 1 μg of total RNA was used to generate complementary DNA (cDNA) using a PrimeScript™ RT reagent Kit with gDNA Eraser (Perfect Real Time) kit (TaKaRa, Japan). Gene expression levels were analysed by qPCR with TB Green Premix Ex Tag II (TaKaRa, Japan). Ubiquitin (UBQ) was used as reference gene to calculate the relative levels of gene expression. The qPCR program was as follows: 95 °C for 30 s; 40 cycles of 95 °C for 5 s, 60 °C for 35 s; 95 °C for 1 min, 55 °C for 30 s, 95 °C for 30 s. All the primers used are listed in Table S8. In addition, the genomic DNA for promoter cloning, transgenic and mutant identification was extracted by a CTAB method (Rogers and Bendich, 1985 (link)).
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6

Evaluating NF-κB and I-κBα mRNA Levels

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The mRNA levels of NF-κB and I-κBα were evaluated by qRT-PCR. RAW 264.7 cells stimulated with lipopolysaccharide (LPS, 100 ng/mL) were seeded in 6-well plates at the density of 1×105 cells/well and incubated overnight. The culture medium was replaced by the fresh medium containing Dsp or LdCaPd NPs (the sum of the concentrations of Dsp and Dex in LdCaPd NPs was set as the incubation concentration, which was equal to the concentration of Dsp, namely 100 nM), and incubated for 24 h. Then, the total RNA was isolated from cells by the TRIzol reagent (Invitrogen, Carlsbad, California, USA), followed by measuring its concentration using a NanoDrop spectrometer (ND-2000, Thermo Scientific, USA). The qRT-PCR was performed on a CFX96 real-time PCR detection system (Bio-Rad, Hercules, California, USA) by using TB Green Premix Ex Tag II (TaKaRa Bio Inc., Japan) with 25 μL reaction mixtures. The relative mRNA expression levels of NF-κB and I-κBα were calculated by specific primers normalized to GAPDH according to the 2−ΔΔCt method (enlisted in Table S1).
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7

Quantifying Gene and microRNA Expression

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The expression levels of ZFAS1, CCND2 and miR‐150‐5p were determined using qRT‐PCR. Total RNA from the left ventricular tissue and cardiomyocytes was extracted using the TRIzol reagent (Invitrogen), first‐strand complementary DNA was extracted using the PrimeScript RT Reagent Kit with gDNA Eraser and TB Green Premix Ex Tag II (TaKaRa Bio, Japan), and miRNA was extracted from total RNA using the Mir‐X miRNA First‐Strand Synthesis Kit and Mir‐X miRNA qRT‐PCR TB Green Kit (TaKaRa Bio, Japan). β‐Actin was used as an internal control in the determination of ZFAS1 and CCND2 expression, whereas U6 was used in the case of miR‐150‐5p expression. qRT‐PCR was performed according to the manufacturer's protocol using a QuantStudio 5 Real‐Time PCR System (Thermo Fisher Scientific, USA). The following primer sequences were employed: ZFAS1 (forward: 5′‐ACGTGCAGACATCTACAAC CT‐3′ and reverse: 5′‐TACTTCCAACACCCGCAT‐3′); miR‐150‐5p (forward: 5′‐TCGG CGTC TCCC AACC CTTG TAC‐3′ and reverse: 5′‐GTCG TATC CAGT GCAG GGTC CGAG GT‐3′); and CCND2 (forward: 5′‐AGAGCCACCGGTATGGAGCTGCTGTGCCACGAGGT‐3′ and reverse: 5′‐CTGCAGGCGCGCCGAATTTTTTTTTTAAGTTTCACCCT‐3′).
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8

Transcriptome Analysis by qPCR

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Cells were collected in RLT buffer and then homogenized by QIAshredder (Qiagen #79656). Total RNAs were isolated with RNeasy Mini Kit (Qiagen #74106) following the manufacturer’s guidelines and then reverse-transcribed to cDNA by PrimeScript™ II 1st strand cDNA Synthesis Kit (Takara, #6210A). qPCR was performed using a ViiA 7 Real-Time PCR System (Thermo Fisher Scientific) and using TB Green Premix Ex Tag II (Takara, #RR820). Primers are described in Supplementary Table S3.
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9

Quantitative Real-Time PCR Gene Expression Analysis

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Total RNA was extracted using RNAiso Plus (Takara Bio, Kusatsu, Japan). Purity was assessed through measurement of the A260/A280 ratio. Complementary DNA was synthesized using Prime Script™ RT Master Mix (TaKaRa Bio). Quantitative reverse-transcription PCR (qRT-PCR) was performed using the 7500 Real-Time PCR System (Applied Biosystems, Foster City, CA, USA) with TB Green@ Premix Ex Tag™ II (TaKaRa Bio). The thermocycling conditions were as follows: 95°C for 30 s, 40 cycles at 95°C for 5 s, and 60°C for 35 s. The housekeeping gene was GADPH. Relative gene expression was calculated using 2ΔΔCt. The primer sequences are listed in Supplementary Figure S2.
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