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5 protocols using quantitect cdna reverse transcription kit

1

Quantitative RT-PCR for Gene Expression

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Total RNA was extracted using RNeasy (RNeasy plus kit, Qiagen, Milano, Italy), quantified using Nanodrop 1000 (Thermo Scientific) and 500 ng were reverse transcribed, prior to gDNA removal, to obtained cDNA using the QuantiTect cDNA reverse transcription kit (Qiagen). Quantitative real-time polymerase chain reaction (qRT-PCR) was performed using the CFX96 Touch Real-Time PCR Detection System (Biorad) using Taqman gene expression assay (Applied Biosystem, Thermo Fisher Scientific). The probes used are HKII (Hs0060686_m1) and GLUT1 (Hs00892681_m1). Data were normalized on Glyceraldehyde 3-Phosphate Dehydrogenase GAPDH (Hs02786624_g1) and TATA-Box Binding Protein TBP (Hs00427620_m1). The relative quantity was determined using ΔΔCt by the CFX Maestro software (BioRad).
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2

RNA Expression Analysis of m6A Regulators

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For qRT PCR, 1 μg of RNA was retrotranscribed using the Quantitect cDNA reverse transcription kit (Qiagen). Quantitative real-time PCR was performed using PrimeTime® Gene Expression Master Mix and the following probes (all IDT): Mettl3 (Mm.PT.58.10309074), Mettl14 (Mm.PT.58.33500780), Mettl16 (Mm.PT.58.9941116), Alkbh5 (Mm.PT.58.6928987), Fto (Mm.PT.58.32888407), and Pcif1 (Mm.PT.58.9572065). TaqMan probes for housekeeping genes Gapdh (Mm99999915_g1) and Hprt (Mm03024075_m1), were from Thermo Fisher.
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3

Circadian Rhythms Gene Expression Analysis

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The tissue was processed for RNA extraction using Qiazol extraction and RNeasy Micro Kit (QIAGEN). Concentrations of mRNA were determined using spectrophotometry with samples diluted to the same final concentration. Immediately following extraction, mRNA was treated with Ambion DNase treatment and removal (Life Technologies) and cDNA synthesis was performed with QuantiTect® cDNA reverse transcription kit (QIAGEN). Reverse-transcription qPCR assays were performed using TaqMan chemistry commercially available validated assays from Life Technologies. Transcripts were amplified on a 7500 Fast Real-Time PCR System by Applied Biosystems (Life Technologies) using TaqMan probes for Rn18s (control gene; Mm03928990_g1), Per1 (Mm00501813_m1), Per2 (Mm00478099_m1), Bmal1 (Arntl1) (Mm00500226_m1), Nr1d1 (Rev-erbα) (Mm00520708_m1), Clock (Mm00455950_m1), Cckar (Mm00438060_m1), Cckbr (Mm00432329_m1). Samples were run in triplicate with a standardized 5 ng (2.5 ng / μL × 2 μL) of cDNA and compared using the ΔΔCT method of relative quantification, with Rn18s used as the control housekeeping gene and ZT0 values as the relative target. Kruskal-Wallis test with post-hoc multiple comparison was performed for statistical analysis.
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4

Antimicrobial Effects of Herbal Extract

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Herbal medicine markets in Mashhad, Iran, provided fresh aerial parts of A. millefolium. Sigma Aldrich (Germany) supplied soybean lecithin with a purity of 99%. As a food-borne pathogen, C. jejuni (RTCC 1097) was provided from Razi Vaccine and Serum Research Institute, Karaj, Iran (Gharib Naseri et al., 2012 ; Ebrahimi et al., 2016 (link)). As part of the gene expression analysis, the RNeasy Mini kit from Qiagen (Hilden, Germany), SYBR Green PCR Master Mix from Qiagen (Hilden, Germany), cDNA Quantitect Reverse Transcription Kit (Qiagen, Hilden, Germany), and SYBR Green PCR Master Mix from Qiagen (Hilden, Germany) were utilised. In this study, DNA was extracted using the QIAamp DNA Stool Mini Kit from Qiagen, Hilden, Germany. Besides these, Merck (Germany) provided the rest of the reagents.
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5

Quantitative PCR Analysis of Retinal Genes

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Total RNA from neuroretina and RPE samples was extracted using High Pure RNA tissue kit (Roche) according to the manufacturer’s instructions. After spectrophotometric quantification of RNA using NanoDrop1000 (Thermo Fisher Scientific), reverse transcription was carried out using cDNAQuantiTect® reverse transcription kit (Qiagen, Hilden, Germany), according to manufacturer’s instructions. cDNA amplification was performed by using 1 μg of RNA as template. Approximately 100 ng of cDNA was used for qPCR. Specific primers for Prpf31 (Mm01329809_m1, Thermo Fisher Scientific), Recoverin (Mm00501325_m1, Thermo Fisher Scientific), Rpe65 (Mm00504133_m1, Thermo Fisher Scientific) and Hspa4l (Mm00495441_m1, Thermo Fisher Scientific) were used. The qPCR was performed using TaqMan® Gene Expression Real Time qPCR assays (Life-Technologies, California, USA) according to the manufacturer’s instructions, using a Thermal Cycler C100 (Bio-Rad). The average cycle threshold (CT) of fluorescence units was used to analyze the mRNA levels. Prpf31, Recoverin, Rpe65 and Hspa4l mRNA levels were normalized by Gapdh RNA levels. Quantification was calculated as: mRNA levels (percent of control) = 2Δ(CT) with Δ (CT) = CT(Prpf31/Recoverin/Rpe65/Hspa4l)- CT(Gapdh).
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