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8 protocols using cellamp direct tb green rt qpcr kit

1

HaCaT Cell-Based Polyphenol MV Assay

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Human adult high-calcium low-temperature (HaCaT) cells (#300493; CLS Cell Lines Service, Eppelheim, Germany) [23 (link)] constitute an immortalized keratinocyte cell line established from the long-term primary culture of human adult skin keratinocytes under specific Ca2+ concentrations and temperature conditions. HaCaT cells were cultivated in MG-30 (DMEM, high glucose, ready-to-use, with serum, CLS Cell Lines Service), supplemented with penicillin-streptomycin (Sigma-Aldrich; penicillin (50 units/mL) and streptomycin (50 µg/mL)) at 37 °C, 5% CO2. In 96-well plates, HaCaT cells (4 × 104 cells/well) were seeded and cultured for 24 h at 37 °C, 5% CO2. After the initial 24 h, each well received 10 µL of isolated microvesicles (MVs) (with or without polyphenols; protein concentration adjusted to 0.4 µg/µL) and was incubated for 6 h at 37 °C, 5% CO2. Dulbecco’s PBS (DPBS; Thermo Fisher Scientific) served as the control. A CellAmpTM Direct TB Green RT-qPCR Kit (TaKaRa Bio Inc.) was utilized for cell lysis, reverse transcription reactions, and real-time RT-PCR following the manufacturer’s protocol. The glyceraldehyde 3-phosphate dehydrogenase (GAPDH) gene was used as an internal standard to normalize mRNA levels among the test samples. The expression level of each gene is presented relative to the expression level in the control. The primer sequences used are presented in Table 1.
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2

Quantifying Gene Expression in HaCaT Cells

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HaCaT cells were cultured in MG-30 (DMEM High Glucose ready-to-use, with serum, CLS Cell Lines Service, Eppelheim, Germany) supplemented with 50 units/mL of penicillin and 50 μg/mL of streptomycin (Thermo Fisher Scientific, Waltham, MA, USA) at 37 °C under 5% CO2. HaCaT cells were seeded at 4.0 × 104 cells/well in a 96-well plate and cultured at 37 °C in 5% CO2 for 24 h. Isolated MVs (10 µL) were added and incubated at 37 °C in 5% CO2 for 6 h. For the control, 10 µL of Dulbecco’s PBS (Thermo Fisher Scientific, Waltham, MA, USA) was used instead of MVs. Cell lysis and reverse transcription reactions were performed using the CellAmpTM Direct TB Green RT-qPCR Kit (TaKaRa Bio Inc., Shiga, Japan). The real-time PCR reaction was performed using Thermal Cycler Dice® Real-Time System II (TaKaRa Bio Inc., Shiga, Japan). The glyceraldehyde 3-phosphate dehydrogenase (GAPDH) gene was used as an internal standard to correct differences in the amount of mRNA between samples. The fold change value with a logarithm transformation [log 2 (2–ΔΔCt)] was calculated. The sequences of the primers are shown in Table 2.
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3

Comprehensive qRT-PCR Analysis of Gene Expression

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RNA was extracted using a RNeasy Plus Mini Kit (Qiagen, Hilden, Germany). Reverse transcription was performed using a High-Capacity cDNA Reverse Transcription kit (Applied Biosystems, Foster City, CA, USA), and real-time RT-PCR analysis was performed using SYBR Green I (Roche Diagnostics, Basel, Switzerland) on a LightCycler® 96 (Roche Diagnostics). Primer sequences and annealing temperatures are provided in Table 1. Gene expression data were normalized to the housekeeping gene encoding hypoxanthine phosphoribosyltransferase (HPRT) 1 and expressed as a ratio of the values obtained for WT mice and control RAW264.7, respectively.
The CellAmpTM Direct TB Green RT-qPCR Kit (TAKARA Bio, Shiga, Japan) was used for primary cultured stellate cells according to the manufacturer’s protocol. Gene expression data were normalized to hypoxanthine phosphoribosyltransferase 1 and expressed as a ratio of the values obtained for the CM from PBS-treated-RAW264.7 cells in addition to LPS (Sigma-Aldrich, St. Louis, MO, USA).
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4

shRNA-mediated knockdown of Polq gene

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The shRNA target sequences were 5′-GAATATGAGTGATAGTATACT-3′ (Polq) and 5′-CAACAAGATGAAGAGCACCAA-3′ (scrambled, negative control). To confirm knockdown, the puromycin-selected transfectants were directly subjected to RT-qPCR analysis using the CellAmp™ Direct TB Green® RT-qPCR Kit (TaKaRa Bio Inc., Shiga, Japan) at 3 days after transfection. The primers for RT-qPCR were as follows: Polq, 5′-GACTCTGGGTTCCACCAGAAG-3′ and 5′-GGCCTGGTAAAGGATGCAAG-3′, Actb, 5′-TTCTACAATGAGCTGCGTGTGG-3′ and 5′-ATGGCTGGGGTGTTGAAGGT-3′.
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5

Quantitative RNA Expression Analysis

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Total RNA was extracted from the cells using TRIzol reagent (Thermo Scientific, Cat# 15596018). Then, the RNA was quantified using Nanodrop. The RNA was reverse-transcribed into DNA using a Prime Script RT Reagent Kit (Takara, Cat#RR036A) following the manufacturer’s instructions. Isolated DNA was subjected to qRT-PCR analysis using the CellAmp™ Direct TB Green® RT-qPCR Kit (Takara, Cat# 3735A). Primer sequences are listed in Additional file 4: Table S4.
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6

Direct RT-qPCR from Aortic Valve Tissues

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The CellAmp™ Direct TB Green™ RT-qPCR kit (Takara Bio,
Inc.) was used to perform qPCR without the need for RNA extraction from aortic
valve tissues of mice and pAVICs. RT was performed and gene expression was
detected on an ABI QuantStudio 7 Flex Real-Time PCR system (Applied Biosystems;
Thermo Fisher Scientific, Inc.). The primers for mouse or porcine target genes
were listed in Table 1. Relative gene
expression data was normalized against GAPDH via the
2−ΔΔCq method.
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7

Quantifying vlmRNA Expression in HEK293 Cells

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HEK293 cells seeded in 96-well plates at 5 × 104 cells per well and cultured overnight were transfected with 200 ng of vlmRNA using 0.5 μl of Lipofectamine 2000 or left untransfected. At 5 h posttransfection, the transfection mixture was removed and fresh medium was added. At 24 h posttransfection, total RNA was isolated and reverse-transcribed into cDNA with a random primer using a CellAmp Direct TB Green RT-qPCR Kit (Takara Bio). The amounts of cDNAs for the vlmRNAs were quantified using a CellAmp Direct TB Green RT-qPCR Kit and a qPCR Thermal Cycler (AriaMx, Agilent). The primers used for amplification of the cDNAs containing the ZsG coding region by real-time PCR were as follows: forward primer: 5′-CCCCGTGATGAAGAAGATGA-3′, reverse primer: 5′-GTCAGCTTGTGCTGGATGAA-3′. Copy numbers were determined by a standard curve method.
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8

Osteoclast Differentiation and Marker Expression Analysis

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To evaluate the expression of osteoclast markers, RAW 264 cells were seeded at 1 × 103 per well in a 96-well plate and induced using 100 ng/mL sRANKL with or without Kampo medicine to differentiate into osteoclasts for one, three, or five days. qPCR analysis was performed using the CellAmp™ Direct TB Green® RT-qPCR kit (TaKaRa, Kusatsu, Japan) and Rotor-Gene Q real-time PCR system (QIAGEN, Dusseldorf, Germany) according to the manufacturer’s instructions. To verify the specificity of each primer, a melting-curve analysis was performed by fluorescence every 0.5 °C from 60 °C to 95 °C. The absence of contamination from either genomic DNA amplification or primer dimer formation was ensured with a Milli-Q water template control. Gene expression values of markers were normalized to Gapdh. The sequences of the gene-specific primer pairs can be found in Table S2.
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