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6 protocols using rox reference dye

1

Quantitative Real-Time PCR Analysis of Gene Expression

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Total cellular RNA was isolated using TRIzol Reagent (cat. 15596026, ThermoFisher Scientific). cDNA was then synthesized from 1 μg of RNA with the RevertAid™ H Minus First Strand cDNA Synthesis Kit (cat. K1632, ThermoFisher Scientific). Gene expression versus β-actin was evaluated by RT-PCR on a MX3000P Real-Time PCR System (Agilent Technology, Milan, Italy). The sequences of the oligonucleotide primers are reported in Table 2. PCR primers were designed using Beacon Designer 4 software (version 4.0, Agilent Technology) from published sequence data stored in the NCBI database. PCR reactions were performed in a total volume of 20 μL, which contained 25 ng of cDNA, 1X Brilliant II SYBR® Green QPCR Master Mix (cat. 600828, Agilent Technology), ROX Reference Dye (cat. 600804, Agilent Technology), and 600 nM of specific primers. The thermal cycling conditions were 1 cycle at 95 °C for 5 min followed by 45 cycles at 95 °C for 20 s and 60 °C for 30 s. In order to verify the possible coamplification of unspecific targets, melting curves were performed for all of the primer pairs in standard conditions. The data required for carrying out a comparative analysis of gene expression were obtained by means of the 2−(ΔΔCT) method [34 (link)].
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2

Quantitative PCR for S. pyogenes and Bacteria

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Quantification of S. pyogenes [38 (link)] and 16S rRNA genes [39 (link)] was performed using hydrolysis probe chemistry. The S. pyogenes assay is commercially available from Biosearch Technologies (Novato, CA). For each sample duplicate 25 μL reactions were run, each containing: 12.5 μL Brilliant® qPCR Master mix (Agilent Technologies, Santa Clara, California), 25 μg BSA (Sigma-Aldrich, Brøndby, Denmark), appropriate concentration of primers and TaqMan® probes (S. pyogenes: 400 nM primers and 100 nM probe, 16S rRNA: 900 nM primers and 200 nM probe), 0.75 μM ROX reference dye (Agilent Technologies) and 2 μL of template DNA. Measurements were obtained by absolute quantification using genomic DNA isolated from S. pyogenes (DSM 20565) and P. aeruginosa (DSM 1253) for total bacteria quantification. The number of isolated genomes was calculated based on DNA concentration (Quant-iT™ dsDNA Assay Kit (Invitrogen)) and genome size estimated to be 1.8 Mbp for S. pyogenes and 6.5 Mbp for P. aeruginosa (http://img.jgi.doe.gov/cgi-bin/pub/main.cgi). Dilution series of the genomic DNA covered a range of 106-100 genome copies. Reactions were run on an Mx3005P (Agilent Technologies) with the following program: 10 min at 95 °C, followed by 40 cycles of 30 s at 95 °C, 1 min at 60 °C.
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3

Quantification of Glyoxalase I Expression

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Glyoxalase I expression vs β-actin was evaluated by quantitative real-time TaqMan PCR analysis (qRT–PCR) on a MX3000P Real-Time PCR System (Agilent Technology). The sequences of oligonucleotide primers and TaqMan probes used for qRT–PCR were as follows: GI: 5′-CTCTCCAGAAAAGCTACACTTTGAG-3′ (sense, 400 nM), 5′-CGAGGGTCTGAATTGCCATTG-3′ (antisense, 400 nM), 5′-FAM-TGGGTCGCATCATCTTCAGTGCCC-TAMRA-3′ (TaqMan Probe, 200 nM); β-actin: 5′-CACTCTTCCAGCCTTCCTTCC-3′ (sense, 600 nM), 5′-ACAGCACTGTGTTGGCGTAC-3′ (antisense, 600 nM), 5′-TEXASRED-TGCGGATGTCCACGTCACACTTCA-BHQ-3′ (TaqMan Probe, 200 nM). All PCR primers and probes were designed using Beacon Designer 4 software (Stratagene, Santa Clara, CA, USA), starting from published sequence data supplied by the NCBI database. The PCR reactions were performed in a total volume of 25 μl, containing 250 ng of cDNA, 1 × Brilliant QPCR master mix (Agilent Technology), 0.5 μl of ROX Reference Dye (Agilent Technology) and a concentration of specific primers and probes. The thermal cycling conditions were as follows: 1 cycle at 95 °C for 10 min, followed by 45 cycles at 95 °C for 20 s and 55 °C for 1 min. Data for comparative analysis of gene expression were obtained using the ΔΔCt method (Livak and Schmittgen, 2001 (link)).
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4

Quantifying Gene Expression by RT-PCR

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Total cellular RNA was isolated using TRIzol Reagent (cat. 15596026, ThermoFisher Scientific). cDNA was then synthesized from 1 µg of RNA with the RevertAid™ H Minus First Strand cDNA Synthesis Kit (cat. K1632, Thermo Fisher Scientific). Gene expression versus β-actin was evaluated by RT-PCR on a MX3000P Real-Time PCR System (Agilent Technology, Milan, Italy). The sequences of the oligonucleotide primers are reported in Table 1. PCR primers were designed using Beacon Designer 4 software (version 4.0, Agilent Technology) from published sequence data stored in the NCBI database. PCR reactions were performed in a total volume of 20 µL, which contained 25 ng of cDNA, 1X Brilliant II SYBR® Green QPCR Master Mix (cat. 600828, Agilent Technology), ROX Reference Dye (cat. 600804, Agilent Technology), and 600 nM of specific primers. The thermal cycling conditions were 1 cycle at 95 °C for 5 min, followed by 45 cycles at 95 °C for 20 s and 60 °C for 30 s. In order to verify the possible co-amplification of the unspecific targets, the melting curves were performed for all primer pairs in standard conditions. The data required for carrying out a comparative analysis of gene expression were obtained by means of the 2-(∆∆CT) method [33 (link)].
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5

Quantifying Gene Expression via RT-PCR

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Total RNA was extracted using the Qiagen Allprep DNA/RNA mini kit (cat.#80204). A total of three micrograms of total RNA were reverse-transcribed using SuperScript II Reverse Transcriptase (Life Technologies) to synthesize cDNA. Quantitative RT-PCR was performed on a Stratagene Mx3000P using 2× Brilliant III SYBR Green qPCR Master Mix plus ROX reference dye (Agilent Technologies). The thermal profiles were set according to the manufacturer’s protocol. The mRNA levels were normalized to Hprt1: (Forward primer: CCTAAGATGAGCGCAAGTTGAA, reverse: CCACAGGACTAGAACACCTGCTAA), PI3Kca: (Forward primer: CCACGACCATCTTCGGGTG, reverse: ACGGAGGCATTCTAAAGTCACTA) H19: (Forward primer: GGAATGTTGAAGGACTGAGGG, reverse: GTAACCGGGATGAATGTCTGG), Igf2: (Forward primer: TCAGTTTGTCTGTTCGGACC, reverse: CACTCTTCCACGATGCCAC).
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6

RNA Extraction and RT-qPCR Analysis

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Total RNA was extracted with RNeasy (Qiagen (https://www.qiagen.com/gb/), Manchester, United Kingdom) and reverse transcribed using QuantiTect reverse transcription (Qiagen) as per manufacturer's instructions. Real‐time quantitative polymerase chain reaction (RT‐qPCR) was performed with Brilliant II SYBR green reagents and a ROX reference dye (Agilent Technologies, (www.genomics.agilent.com), La Jolla, California, USA) using the ViiA7 qPCR system. Primer sequences were Yap (5′‐TGAGCC CAAGTCCCACTC‐3′; R‐5′‐TGTGAGTGTCCCAGGAGAAA‐3′), Taz (5′‐TATCCCAGCCAAATCTCGTG‐3′, R‐5′‐TTCTGCTGGCTCAGGGTAC T‐3′) or as described 43.
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