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49 protocols using faststart dna master sybr green 1

1

Curcumin and Endoxifen Cytotoxicity Evaluation

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Curcumin was purchased from Plamed Green Science Limited (China). Endoxifen was purchased from Tocris Bioscience (USA). Beta estradiol, glutaraldehyde, poly-L-lysine were purchased from Sigma-Aldrich Ltd (Singapore). Dimethylsulfoxide (DMSO) was purchased Vivantis (Malaysia), DMEM-high glucose, FBS heat-inactivated, Penicillin/Streptomycin, Fungizone, were purchased from Biowest (USA). MTS assay kit was purchased from Promega (USA). High Pure RNA isolation kit, Transcriptor First Strand cDNA Synthesis kit, FastStart DNA master SYBR Green I were purchased from Roche (USA). Primers for E-cadherin, TGF-β1, vimentin and β-actin were purchased from First-base (Singapore), Human TGF-β1 ELISA kit and Coomassie Plus (Bradford) Assay Kit were purchased from invitrogen (USA).
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2

Validating Transcriptome Data by qPCR

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To validate the transcriptom dataset, five random transcripts from immune-related genes were selected for real-time qPCR confirmation. Primer sequences were designed using (http://fokker.wi.mit.edu/primer3/) and the related information are shown in S4 Table. According to the FastStart DNA Master SYBR Green I (Roche Diagnostics) protocol, the reactions were run on LightCycler system (Roche Diagnostics) using 20 mL reaction system. Reaction procedures were: 95°C 10 s, 45 cycles at 60°C 5 s, 72°C 20 s with fluorescence reading. Immediately following PCR, the machine performed a melting curve analysis by gradually increasing the temperature (0.1°C/s) while measuring the intensity of fluorescence emission. The mRNA expression of each gene was normalized to 18S rRNA expression (accession no. AY319433; 18S rRNA-F, 5’-CTC ACG GAA AGA GCG CGT TTA-3’, 18S rRNA R: 5’-GAC TTG CCC TCC AAT AGA TC-3’) as a reference gene. Each sample was analyzed in triplicate and the data were calculated as the mean ± standard deviation (SD) of relative mRNA expression.
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3

Quantitative RT-PCR of SGLT2 in Rat Kidneys

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Total RNA was isolated from the rat whole kidneys with the TRIzol® Reagent (Life Technologies, Carlsbad, CA). RNA was quantified by spectrophotometry, and cDNA synthesis was performed on 3 µg of RNA with SuperScript® III Reverse Transcriptase (Life Technologies, Carlsbad, CA). For quantitative polymerase chain reaction (PCR), 45 ng of cDNA served as a template for PCR amplification using Brilliant SYBR green QPCR master mix according to the manufacturer's instructions (FastStart DNA Master SYBR Green I, Roche Molecular Biochemicals, Mannheim, Germany). The SGLT2 gene-specific sequences used were the forward primer 5′-CATTGTCTCAGGCTGGCACTGG-3′ and the reverse primer 5′-GGACACTGCCACAATGAACACC-3′, respectively19) (link). The thermal profile of the LightCycler® Instrument (Roche Molecular Biochemicals, Mannheim, Germany) was optimized with an initial denaturation of 10 minutes at 95℃ and 45 amplification cycles with each 10 seconds at 95℃, 10 seconds at 58℃ and 10 seconds at 72℃. The comparative Ct method was used to determine the relative amounts of target-mRNA levels calculated for each sample by expressing the target-mRNA level as a percentage of GAPDH mRNA levels. Ct ratios were analyzed using the LightCycler® Software (Version 4.05). Specificity was ensured by postrun melting curve analysis.
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4

Quantitative Real-Time RT-PCR of LRG1 and GAPDH

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The primer sequences were customized by Sigma‐Aldrich, as follows: LRG1 (accession no. NM_052972) and GAPDH (accession no. NM_002046, NM_001256799, NM_001289745, NM_001289746) as the internal control. Quantitative real‐time RT‐PCR (qRT‐PCR) was carried out with FastStart DNA Master SYBR Green I (Roche Diagnostics, Basel, Switzerland) and the LightCycler System (Roche Diagnostics).
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5

Total RNA Extraction and qPCR Analysis

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Total RNA was extracted from the DG using the ReliaPrep RNA Miniprep System (Promega), and subjected to reverse transcription with Superscript VILO (Invitrogen), and followed by real-time PCR on a LightCycler (Roche) using the Fast Start DNA Master SYBR Green I (Roche). Expression levels of target genes were normalized to the levels of 18S rRNA. Primer sequences are shown in Table 1. The specificity of each primer set was confirmed by checking the product size by gel electrophoresis.
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6

Quantifying IL15 and IL15RA Expression

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Total cellular RNA was isolated from PBMCs, BFCs or CD14+-isolated monocytes using the High Pure RNA Isolation Kit (Roche, Mannheim, Germany) according to the manufacturer’s instructions and 1 μg was reverse transcribed with random hexanucleotides and AMV reverse transcriptase (Roche) in a final volume of 20 μL for 1 h at 42 °C. For skin biopsies, RNA was extracted using TriReagent® (Molecular Research Center, Inc. Cincinnati, OH, USA) according to the manufacturer’s instructions, and 500 ng was used for reverse transcription.
The expression of human IL15 and IL15RA genes was analyzed by PCR amplification of 1 μL aliquots of the resulting cDNAs in a total volume of 15 μL, in a Light Cycler (Roche) with FastStart DNA Master SYBR Green I (Roche). Standard curves for target mRNA expression were generated by amplifying 10-fold serial dilutions of known quantities of the specific PCR product. Quantification of target gene expression was obtained using Light Cycler system software version 4.05 (Roche, Mannheim, Germany). B2M was used as a housekeeping reference gene, except for experiments involving skin biopsies, in which ARF5 was used as a reference. Relative units estimated from the quantification (Rq) represent the ratio between specific mRNA molecules/μL cDNA and molecules of B2M (or ARF5) mRNA/μL cDNA.
The primers used are shown in Table S3 in the Supplementary Materials.
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7

Quantifying Gene Expression in Drosophila

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The expression levels of Ada2b, RpL32, Drosomycin, CG6675, and CG33462 were determined using RT-PCR. To prepare fly samples, Ml or Sa suspension (OD = 1) was injected into flies as described above. The flies were collected at 4, 8, and 16 h post-challenge infection. Total RNA was extracted from three flies for each sample, and three samples were analyzed as biological replicates for each experimental condition. Complementary DNA (cDNA) was synthesized from total RNAs using ReverTra Ace (Toyobo), following the manufacturer’s instructions. RT-PCR analysis was performed using the Thunderbird Next SYBR qPCR Mix kit (Toyobo) or FastStart DNA Master SYBR Green I (Roche) with Light Cycler 96 (Roche). The primers used for RT-PCR analysis are listed in S6 Table. The relative gene expression was quantified using the R program. The expression data were statistically compared using ANOVA, followed by Tukey’s HSD post-hoc test with the R program.
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8

Real-Time qPCR Analysis of Gene Expression

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Total RNA was extracted from the cells using the RNeasy Plus Mini Kit (QIAGEN K.K., Tokyo, Japan). Reverse transcription was performed on 0.5~1.0 µg of total RNA using the PrimeScript® RT reagent Kit (TAKARA Bio. Inc. Shiga, Japan). Real-time quantitative PCR was performed on cDNA aliquots with the FastStart DNA Master SYBR Green I and the LightCycler (Roche Diagnostics, Mannheim, Germany). The sequences of the oligonucleotide primer pairs used to amplify the mRNA in the mouse and human cells are shown in Table 1. PCR amplification began with a 10 min pre-incubation step at 95°C, followed by 40 cycles of denaturation at 95°C for 10 s, annealing at 62°C for 10 s, and elongation at 72°C (Table 1). The relative concentration of PCR product derived from the target gene was calculated using the LightCycler System software. A standard curve for each run was constructed by plotting the crossover point against the log concentration. The concentration of target molecules in each sample was then calculated automatically by reference to this curve (r = −1.00), and the results were standardized to the expression of β-actin. The specificity of each PCR product was assessed by melting curve analysis.
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9

Quantifying Arrestin Gene Expression

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To evaluate arrestin mRNA levels, these primers were specifically designed to detect and quantify cDNA sequences without detecting genomic DNA. The Fast-Start DNA Master SYBR Green I (Roche Ltd., SWISS) was used as fluorescent reporter dye to detect amplification products in 7500 Fast Real Time PCR System (Applied Biosystems Inc. Carlsbad, CA, USA) using the following cycling conditions: denaturation at 95°C for 10 min and 40 cycles of reactions of denaturation at 95°C for 10 s, annealing at 58°C for 30 s, and elongation at 72°C for 30 s. Each sample was tested in triplicate to ensure statistical significance. The PCR efficiency (E%) of gene was derived from perforin (96.2%) and b-Actin (95.4%) respectively. The relative quantification of arrestin gene expression was performed using the comparative Ct method. The Ct value is defined as the point where a statistically significant increase in the fluorescence has occurred. The number of PCR cycles (Ct) required for the ROX intensities to exceed a threshold just above background was calculated for the test and reference reactions. In all experiments, β-Actin was used as the endogenous control. Results were analyzed in a relative quantitation study with the vehicle treated.
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10

Quantification of Connexin Genes in Mammary Cells

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Total RNA was isolated with QIAGEN RNeasy Mini Kit (Valencia, CA). For cDNA synthesis, 20 ng of total cellular RNA was used to synthesize cDNA using SuperScript III First-Strand Synthesis System (Invitrogen, Carlsbad, CA). Primers for Cx26, Cx30, Cx32, Cx43, β-casein and whey acidic protein were used. Cx26 (sense: gaatgtatgctacgaccacca, antisense: ctttcctgagcaatacctaacg); Cx30 (sense: gggtaccacctaccctgggtac, antisense: tgcattctggccactatctgag); Cx32 (sense: aatgctacggcttgaggggcatg, antisense: gcctgctcaccggcataggag); Cx43 (sense: gttcagcctgagtgcggtctac, antisense:ggctctgctggaaggtcgctgatc); β-casein (sense: gtggcccttgctcttgcaag, antisense: agtctgaggaaaagcctgaac); WAP (sense: atgcgttgcctcagcc, antisense: gacaggcagggatggc). Real-time PCR was performed using LightCycler System (Roche Diagnostics, Indianapolis, IN) according to the manufacturer’s instructions. Fast Start DNA Master SYBR Green I (Roche Diagnostics, Indianapolis, IN) was used for PCR reaction. PCR data were analyzed with LightCycler Software ver.3 (Roche Diagnostics, Indianapolis, IN). Relative signals between Cxs and 18s rRNA were quantified.
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