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6 protocols using trizol solution

1

Quantifying Gene Expression in Aortic Valve

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Total RNAs was extracted from aortic valve tissues using the TRIzol solution (217004, Qiagen). cDNA was reverse transcribed from 1μg RNAs using the Superscript II reverse transcriptase Kit (1708891, Bio-Rad). Quantitative reverse transcription real-time PCR (RT-qPCR) was performed on the Applied Biosystems 7500 real-time PCR system using the Power SYBR Green PCR Master Mix (4367659, Life Technology) containing gene specific primers (S1 Table). The fold change of mRNA level was normalized to the level of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and calculated using the 2-ΔΔCT method. RT-qPCR analysis was performed for 5 or 8 individual samples per group in technical triplicates.
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2

Quantitative Analysis of Gene Expression

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Total RNA was extracted from PBMCs, PFMCs, and ESCs using Trizol solution (Qiagen) based on the manufacturer's protocol. Quantity and purity of the extracted RNA were measured using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific), and RNA integrity was assessed by electrophoresis on 2% agarose gel. For cDNA synthesis, 1 μg of RNA was reverse transcribed into cDNA using a Revert Aid First Strand cDNA Synthesis Kit (Thermo Fisher Scientific) according to the protocol. The qRT‐PCR was performed in duplicate using Rotor‐Gene 3000 (Corbett Research) with the SYBER premix Extaq (Biofact). The mRNA expression of MCP‐1, HGF, and IGF‐1 were normalized using glyceraldehyde 3‐phosphate dehydrogenase (GAPDH) mRNA as a housekeeping gene. The sequences of the primers and size of amplicons are shown in Table 1. Briefly, 10 μl SYBER premix Extaq (Biofact), 1 μl primer pairs, 1 μl cDNA template, and 8 μl DNase‐free water were amplified in Rotor‐Gene 3000 with cycling conditions as 95°C step for 15 min (initial denaturation and activation of enzyme), followed by 40 cycles of 95°C for 20 s, annealing and elongation at 60°C for 40 s and the melting step at 60 to 99°C. All reactions were run in duplicate.
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3

Lung tissue RNA extraction and analysis

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Approximately 10% of each lobe of lung was snap-frozen at -80°C to preserve RNAs. The lungs were then homogenized in Trizol solution (Qiagen, Hilden, Germany) using a gentleMACS tissue dissociator (Miltenyi Biotec, Bergisch Gladbach, Germany), and total RNA was immediately extracted using the miRNeasy miRNA extraction kit (Qiagen). The isolated total RNA samples containing miRNAs were then subjected to miRNA and gene microarray analyses.
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4

PD-L1 and METTL16 Gene Expression Analysis

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Total RNAs were extracted using the Trizol solution (Qiagen, USA). Then a total of 1 μg RNA was subjected to reverse transcription reactions using a Reverse Transcription kit (Qiagen, USA). PCR amplification was conducted using the SYBR GREEN qPCR mix (Thermo, USA).
PD-L1 forward primer: 5’- TGGCATTTGCTGAACGCATTT-3’,
PD-L1 reverse primer: 5’-TGCAGCCAGGTCTAATTGTTTT-3’;
METTL16 forward primer: 5’-CTCTGACGTGTACTCTCCTAAGG -3’,
METTL16 reverse primer: 5’- TACCAGCCATTCAAGGTTGCT-3’.
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5

Quantitative Gene Expression Analysis

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The TRIzol solution (Qiagen, Switzerland) was used to extract the total RNA from the HUVECs according to the instructions of the manufacturer, followed by transcribing the RNAs to cDNA using the SuperScript III (Takara, Tokyo, Japan) reagent. The SYBR green quantitative PCR kit (Takara, Tokyo, Japan) was used to determine the relative expression of target genes, while GAPDH was taken as the negative control. QRT-PCR was performed on the ABI Prism 7500 Fast Sequence Detection System (Applied Biosystems, CA, USA). The 2-ΔΔCt method was used to calculate and quantify the relative expression level of target genes. The following primers were used in this study: LOX-1 (F: 5’-TGATAGAAACCCTTGCTCG-3’, R: 5’- TTGCTTGCTGGATGAAGTC-3’); MCP-1 (F: 5’-GTTGGCTCAGCCAGATGCA-3’, R: 5’-AGCCTACTCATTGGGATCATCTTG-3’); CXCL-2 F: 5’-GGCAGAAAGCTTGTCTCAACCC-3’, R: 5’-CTCCTTCAGGAACAGCCACCAA-3’); eNOS (F: 5’-GTGGCTGTCTGCATGGACCT-3’, R: 5’-CCACGATGGTGACTTTGGCT-3’); Occludin (F: 5’-TACAGCAATGGAAAACCACACT-3’, R: 5’-CAAAGGAATGGGAAACGACTAA-3’); KLF2 (F: 5’-CCAAGAGTTCGCATCTGAAGGC-3’, R: 5’-CCGTGTGCTTTCGGTAGTGGC-3’); GAPDH (F: 5’-GACGGCCGCATCTTCTTGT-3’, R: 5’-CAGTGCCAGCCTCGTCCCGTAGA-3’).
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6

Quantifying Gene Expression in hUC-MSCs

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Total RNA extraction from hUC-MSCs was performed using the Trizol solution (Qiagen, Valencia, CA, USA) and cDNA was obtained from total RNA using an Advantage RT-PCR kit (Clontech, Palo Alto, CA, USA). Table 1 shows the primer sequences used for real-time qPCR. The following genes were examined: Plexin A4 (PLXNA4), Formin 1 (FMN1), Amphiregulin (AREG), Stathmin 2 (STMN2), Serpin Family I Member 1 (SERPINI1), Microtubule-associated protein 2 (MAP2), Neuronal Differentiation 1 (NEUROD1), Glial fibrillary acidic protein (GFAP), Myelin basic protein (MBP), and Neurofilament-L (NF-L).
Real-time qPCR was performed according to the SimpliAmp Thermal Cycler (Applied Biosystems, Foster City, CA, USA), which enables real-time quantitative detection of PCR products based on SYBR green fluorescence due to the incorporation of SYBR green into double-stranded DNA. The results were analyzed by a comparative cycle threshold (CT) method for the quantification of relative gene expression for the housekeeping gene (GAPDH).
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