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25 protocols using rnx plus kit

1

ITGA4 mRNA Quantification in Cells

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Total RNA of 106 cells in each group was extracted using RNX plus kit (SinaClon, Iran) and stored at -80 °C. The RNA concentration was assessed by NanoDrop (Goldenlab, Indonesia) at 260 nm, and then, cDNA was synthesized according to the first strand cDNA synthesis kit instructions (Thermo Scientific, USA). ITGA4 mRNA was quantified by SYBR Green-based real time PCR (Applied Biosystem, USA) using forward (5'-TTCCAGAGCCAAATCCAAGAGTAA-3) and reverse (5 '-AAGCCAGCCTTCCACATAACAT-3') primers. Beta actin (F: 5'-TTCGAGCAAGAGATGGCCAT-3', R: 5'-CACAGGACTCCATGCCCAG-3') was applied as the endogenous control for gene expression analysis.
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2

Total RNA Extraction and cDNA Synthesis

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Total RNA of O. vulgare leaves was extracted using RNX plus™ kit according to the manufacturer's instructions (Sinaclon, Iran). After evaluating the quality and quantity of RNA using 1% agarose gel electrophoresis and nanodrop ND-1000, cDNA was synthesized using Revert Aid™ First Strand cDNA Synthesis Kit (Thermo Fisher Scientific, USA) according to the instructions of the manufacturer (Thermo Scientific, USA). Negative control reactions using reverse transcriptase minus (-RT) and non-template control (NTC), was performed to ensure no genomic DNA contamination and for reagent contamination, respectively.
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3

Investigating TtAQP Gene Expression via qPCR

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An RNX plus kit (Sinaclon, Tehran, Iran) was used for RNA extraction based on the manufacturer’s instructions. The quality and quantity of the extracted RNA were checked using a NanoPhotometer (Implen N50, IMPLEN, München, Germany). Complementary DNA (cDNA) was synthesized by reverse transcriptase (Roche, Mannheim, Germany) based on the manufacturer’s protocols. The expression levels of TtAQP genes were investigated using Maxima SYBR Green/ROX qPCR (quantitative real-time PCR) Master Mix (Thermo Fisher, Illkirch-Graffenstaden, France) based on the manufacturer’s protocol and ABI Step One. The cycling patterns of qPCR were 95 °C for 10 min, then 35 cycles at 95 °C for 15 s, and 60 °C for 60 s. The relative expression of each gene was calculated using the delta delta Ct method [39 (link)]. The expression difference between the treatments and the control sample was calculated based on a t-test. All experiments were performed in three biological replicates.
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4

Quantification of TNF-α in Tissue Homogenate

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For the quantitative determination of TNF-α level in tissue homogenate, a commercial kit (Kermania pars Gene, Kerman, Iran) was used based on the manufacturer's procedure. Absorption was measured via an ELISA reader (BioTek; Winooski, Vermont, USA) at 450 nm. To investigate gene expression, the total RNA was obtained from tissue homogenate by the RNX Plus kit (Sinaclon, Tehran, Iran) according to the manufacturer's instructions. Then, first-strand complementary DNA (cDNA) was produced using cDNA Synthesis kit (Sinaclon, Tehran, Iran), and Real-time PCR was performed using a RotorGene 3000 instrument (Bio-Rad, USA). PCR program was run as follows: denaturation stage at 95 °C for 15 s, annealing stage at 62 °C for 30 s, and elongation stage at 72 °C for 30 s in 40 cycles. The relative gene expression was determined by the 2−ΔΔCt formula. HPRT1 was used as the reference housekeeping gene and the findings were presented as the fold changes relative to the control group.
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5

Liver Tissue RNA Extraction Protocol

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Total RNA was isolated from each liver tissue by RNX-plus Kit (SinaClon, Iran). The samples were frozen in liquid nitrogen and were crushed and homogenized for RNA extraction (Bottje et al., 2009 (link); Kong et al., 2011 (link)). After RNA purification and removal of DNA remnants by DNasel (kit-SinnaGen), the RNA quantity was measured by NanoDrop spectrophotometer ND-1000 (Absorbance 260 and 280 nm) and RNA integrity was validated by agarose-gel electrophoresis.
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6

Quantifying MV RNA Content

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The RNA content of the MVs was extracted using the RNX Plus™ kit (SinaClon, Tehran, Iran). Due to low amounts of extracted mRNAs, the detection of specific mRNA content of MVs was performed according to SinaClon First Strand cDNA Synthesis Kit (SinaClon, Tehran, Iran) and qPCR Master Mix (A320799 Ampliqon, Denmark). Designed primers for specific mRNAs are depicted in supplementary Table 1. Quality control of the primers was carried out by LinReg PCR software (Amsterdam, Netherlands).
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7

RNA Extraction from Cultured Cells

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Total RNA was isolated using the RNX‐PLUSKit (SINACLON, Iran) according to the manufacturer's protocol. The number of 3 × 104 cells of YM‐1 or KYSE‐30 cells were cultured in the flask. After 24 h incubation, cells were treated with DMSO (0.3% as control) or entacapone (IC50 = 140 μM) for 48 h. Then, cells were harvest with trypsin solution and washed twice with PBS. To extract the RNA, briefly, cells were disrupted and homogenized with RNX‐PLUS reagent at room temperature (RT) for 5 min. Then, chloroform was added to the samples and shacked vigorously for 5–10 s, then incubated for 15 min. Subsequently, using centrifugation (12 000 rpm at 4°C for 15 min), the upper aqueous phase containing the nucleic acids was isolated. Then, it was precipitated by adding equal volume of isopropanol followed with incubation for 15 min on ice and centrifugation. The RNA was washed twice by adding 1 ml 75% ethanol, and centrifugation at 7500 rpm at 4°C for 8 min. Finally, the purified RNA samples were dissolved in RNase‐free water and stored at −80°C.
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8

Viral RNA Extraction and cDNA Synthesis

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According to the manufacturer's instructions, viral RNA was extracted from all samples using the RNX-PLUS kit (Sinaclon, Iran). In brief, 1 ml of RNX-PLUS solution and 200 μl of chloroform were added to the tube containing the sample. Then, the mixture was centrifuged at 12000g at 4°C for 15 min. Next, the aqueous phase was transferred to a new tube, and an equal volume of isopropanol was added. The supernatant was discarded after centrifugation, and 1 ml of 75% ethanol was added to the mixture. Afterward, the supernatant was removed, and the sediment was dried at room temperature. The concentration of the RNAs extracted was measured using a spectrophotometer. Following this, complementary DNA (cDNA) synthesis was performed using SinaClon first-strand cDNA synthesis kit according to manufacturer's instructions.
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9

Plasma miRNA Extraction and RT-qPCR

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MicroRNAs were extracted from plasma samples using RNX-Plus kit (SinaClon, Iran) according to the manufacturer`s instructions and 1μg of RNA was reverse-transcribed using the mixture of M-MLV enzyme (Vivantis, Malaysia), 1x RT-enzyme buffer, 400 μM dNTP, and 1μM of specific stem-loop RT primers and incubated at 75 °C for 5 min. The mixture was incubated at 25°C for 15 min, 37°C for 15 min, 42°C for 45 min, and 10 min at 75°C, in a thermal cycler (Eppendorf, Germany). Finally, the obtained cDNAs were stored at −20°C prior to RT-qPCR analyses.
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10

Hippocampal RNA Extraction Protocol

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At the end of the experimental period, the rats were immediately sacrificed under chloral hydrate anesthesia. Brains were extracted from skull and hippocampi were collected immediately and kept in homemade RNAlater solution – for stabilization and protection of cellular RNA- (25 mM sodium citrate, 10 mM EDTA and 70 g of ammonium sulfate/ 100 mL, pH 5.2) at 4°C. Then, the total RNA was extracted from hippocampal tissues by RNX plus Kit (Sinaclon Co, Iran) according to the procedure.
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