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Sybr green 1

Manufactured by Toyobo
Sourced in Japan, China, United States

SYBR Green I is a fluorescent dye used in molecular biology and biochemistry for the detection and quantification of nucleic acids, such as DNA and RNA. It binds to the minor groove of double-stranded DNA, resulting in a fluorescent signal that can be measured using specialized equipment.

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38 protocols using sybr green 1

1

RNA Extraction and Real-Time PCR Analysis

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Total RNA was extracted from AT and serum and quantified (300 ng/μL RNA of each sample), respectively. Reverse transcription was performed using the FSQ-301 kit (TOYOBO, Shanghai, China) according to the manufacturer’s instructions. QRT-PCR system for mRNAs was 10 μL, containing 0.6 μL cDNA, 0.3 μL of each primer, 5 μL 2 × SYBR Green I (TOYOBO, Shanghai, China), 0.2 μL 50 × ROX (TOYOBO, Shanghai, China), 3.6 μL RNA-free water. QRT-PCR system for miRNA was 10 μL, including 0.8 μL cDNA, 0.3 μL of each primer, 5 μL 2 × SYBR Green I (TOYOBO, Shanghai, China) 0.2 μL 50 × ROX (TOYOBO, Shanghai, China), 3.4 μL RNA-free water. QRT-PCR procedures of the mRNAs and miRNAs were: 95 °C for 1 min, followed by 45 cycles, 95 °C for 15 s, 60 °C for 30 s, 72 °C for 30 s, and 72 °C final extension for 30 s. The β-actin gene and U6 were selected as the internal references mRNAs and miRNAs, respectively. All primer sequences are provided in Table 1.
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2

Quantitative RT-PCR for Gene Expression Analysis

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Total RNA was extracted from different tissues using TRIzol (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. Agarose gel electrophoresis (AGE) was used to estimate the integrity of total RNA, and a DU800 spectrophotometer (Beckman Coulter, Miami, FL, USA) was used to quantify the total RNA. Briefly, 300 ng of RNA of each sample was reverse-transcribed using the reverse transcription kit FSQ-301 (TOYOBO, Shanghai, China) following the manufacturer’s instructions. qRT-PCR amplification efficiency was assessed by varying the cDNA template concentration to obtain a relative quantitative standard curve, and specificity was assessed by melting curve. qRT-PCR was performed in three technical iterations with a 10 μL reaction mixture, which contained 5 μL of 2× SYBR Green I (TOYOBO, Shanghai, China), 0.2 μL of 50× ROX reference dye (TOYOBO, Shanghai, China), 0.3 μL of each primer, 1 μL of cDNA, and 3.2 μL of RNA-free water. U6 was chosen as an endogenous control for miRNAs. The qRT-PCR procedure was as follows: 95 °C for 1 min, followed by 40 cycles at 95 °C for 15 s, 60 °C for 30 s, 72 °C for 30 s, and s final extension for 30 s at 72 °C. All primer sequences are provided in Table 1.
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3

Quantitative Analysis of Arih2 Gene Expression

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Quantitative real-time PCR (qRT-PCR) was used to analyze the transcriptional activities of Arih2 gene in each tissue. The qRT-PCR system doses and reaction procedures of the Arih2 gene were the same as the internal reference β-actin (GenBank number: NM205518). The primers used for qRT-PCR were as follows: target gene Arih2: 5′-AGGGACTATGTGGAGAGCCATTACC-3′ and 5′-AAGCAGAAGACCTCATTGCAACGAT-3′; internal reference gene β-actin: 5′-CACCAACTGGGATGATAT-3′ and 5′-CGTACTCCTGCTTGCTGATC-3′. qRT-PCR total system was 20 μl including: 10 μl 1× SYBR Green I (TOYOBO, Shanghai), 0.4 μl 50× ROX reference dye (TOYOBO, Shanghai), 0.6 μl of each primer, 2 μl cDNA and 6.4 μl ddH2O. The reaction procedure was as follows: 95°C/1 min; 40 cycles of 95°C/15 s, 56°C/30 s, 72°C/40 s.
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4

Quantitative Analysis of miR-124a and Target Genes

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Forty-eight hours after transfection with the miR-124a mimics/inhibitors, total RNA of the Mac-T cells was extracted using trizol reagent (Invitrogen). The quantity of RNA was verified by NanoDrop1000 (Thermo Scientific), ensuring the optical density (OD) 260nm/280nm value was between 1.8 and 2.0. Complementary DNA (cDNA) was synthesized using the Primer Script reverse transcription PCR (RT-PCR) kit (Takara). The expressions of miR-124a and target genes were detected on a Bio-Rad CFX Connect instrument (Biorad, America) using the SYBR Green I (TOYOBO, Japan). Primer 6.0 (Premier) was used to design fluorescently labeled primers and reverse transcription primers for quantitative analysis of miR-124a, PECR, and ELOVL2 (enhanced extension of very long chain fatty acid protein 2). The expression of U6 and GADPH (glyceraldehyde-3-phosphate dehydrogenase) was used as a loading control. All primers were synthesized by Shanghai Sangon Biotechnology Company (see Table 1). The relative gene expression was calculated by the 2−ΔΔCt method.
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5

Quantitative Analysis of Cardiac Gene Expression

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Total RNA samples were extracted from cardiomyocytes or myocardium using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). The expression levels of H19, miRNAs including miR-18a-3p, miR-92a-2-5p, miR-93-3p, miR-361-3p, miR-744-3p, and miR-877-3p, Bcl-2, and Bax mRNA were tested by using SYBR Green I (TOYOBO, Osaka, Japan) through the ABI 7500 fast Real Time PCR system (Applied Biosystems, Foster City, CA, USA). β-Actin was used as an internal control of H19, Bcl-2, and Bax. U6 served as an internal control of miRNAs. The relative quantitative expression was determined using the 2−ΔΔCT method. The primers were synthesized by Invitrogen and were listed in Tables S2 and S3.
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6

RNA Extraction and Real-time PCR Analysis

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Total RNA was extracted using RNeasy Mini Kit (Qiagen #74106). cDNA was synthesized using First-Strand cDNA Synthesis kit (Fermentas, St. Leon-Roth, Germany). The real-time PCR reaction kit contained 0.2 μM sense primer, 0.2 μM antisense primer, 12.5 μl SYBR Green I (Toyobo, Osaka, Japan), and 5 μl of previously synthesized cDNA in a total volume of 25 μl. Primers used can be found in supplement materials.
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7

Quantitative Real-Time PCR Analysis of Heat Stress

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For quantitative real-time PCR analysis, samples were prepared from leaves harvested 6 days after heat stress. The samples were frozen in liquid nitrogen and stored at −80 °C. Total RNA was extracted from the samples using TRIpure reagent (Aidlab Biotechnologies, Beijing, China). RNA was converted into first-strand cDNA using the ReverTra Ace qPCR RT Master Mix (TOYOBO, Shanghai, China) and oligo (dT) as the primer. The resultant cDNA was used as the template for quantitative PCR amplification in a Thermal Cycler Dice Real-Time System II (TaKaRa Biotechnology, Dalian, China) with SYBR Green I (TOYOBO) as the fluorescent reporter. Primers were designed to generate 150–250 base pair (bp) fragments using the PRIMER3 software [37 (link)] (Table S3). PCR analysis and detection were performed as described previously [38 (link)]. The 2−ΔΔCT method was employed to analyze the relative gene expression levels using the mean values from three replicates.
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8

Quantitative Analysis of Cardiac Gene Expression

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The total RNA samples were extracted from cardiomyocytes or cardiac tissues using the TRIzol reagent (TaKaRa, Otsu, Shiga, Japan). Total RNA for 500 ng was reverse transcribed to cDNA using Reverse Transcriptase Master Kit (Toyobo, Osaka, Japan) according to the manufacturer’s instructions. Real-time PCR was performed on ABI 7500 fast system (Applied Biosystems, Carlsbad, CA, U.S.A.) using SYBR Green I (Toyobo, Osaka, Japan). GAPDH served as an internal control. The relative quantitation of gene expression was determined using the 2−ΔΔCT method.
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9

Quantifying tRF-5014a Expression

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Reverse transcription was achieved using a reverse transcription kit (Toyobo, Japan) at 42°C for 60 min and then at 70°C for 10 min. The tRF-5014a-specific RT-primer, which was designed by RIBOBIO (Guangzhou, China), was used instead of random primer to detect the level of tRF-5014a. The tRF-5014a-specific forward primer was also designed by RIBOBIO (Guangzhou, China). An ABI 7500 Fast Real-Time PCR system (Applied Biosystems, CA, USA) was used to perform real-time PCR, amplifying and quantifying cDNA using SYBR Green I (Toyobo, Osaka, Japan) according to the manufacturer’s protocols. The expression levels of tRFs were standardized to U6. The relative expression levels of genes were quantified by the 2-ΔΔCT method.
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10

Quantitative Real-Time PCR Analysis of Gene Expression

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Modified 1640 Medium (HyClone)

Dulbecco’s Modified Eagle Medium (DMEM) (HyClone)

Fetal bovine serum (FBS) (Gibco)

CCK8 regent (Beyotime)

Double antibody (penicillin/streptomycin stock) (TBD)

High pure total RNA fast isolation kit with spin column (BIOTEKE)

Recombinant DNase I (RNase-free) (TAKARA)

Recombinant Ribonuclease Inhibitor (TAKARA)

Oligo (dT)18 Primer (TAKARA)

Random Primer (hexadeoxyribonucleotide mix: pd(N)6) (TAKARA)

Reverse Transcriptase M-MLV (RNase H-) (TAKARA)

Deoxynucleotide triphosphate mixture (TAKARA)

SYBR Green I (TOYOBO)

HiScript II Q RT SuperMix for qPCR (+gDNA wiper) (Vazyme)

Hieff TMqPCR SYBR® Green Master Mix (LoW Rox Plus) (Yeasen)

DL 2000 DNA marker (TAKARA)

Annexin V-APC/7AAD kit (Multi Sciences)

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