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7 protocols using sybr premix

1

RNA Extraction and qRT-PCR Analysis

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RNA from the liver tissues or bone marrow macrophages was extracted using TRIzol Reagent (Invitrogen Life Technologies, Carlsbad, California, USA). RNA (2 μg) was reverse transcribed in a final volume of 20 μl using RT2 first strand kit (Qiagen, USA), as specified by the manufacturer, and then subjected to PCR using specific primer sets (S1 Table). qRT-PCR was conducted using an ABI 7500 FAST System (Applied Biosystems, USA). cDNA (100 ng) was subjected to qRT-PCR in a 25 μl reaction volume using SYBR-Premix (Qiagen). The GAPDH gene was amplified for normalization of the cDNA amount used in qRT-PCR. Reactions were carried out in triplicate, and the data were analyzed using the 2−ΔΔCt method.
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2

Odontogenic Differentiation Gene Expression

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The odontogenic differentiation-related gene expression was detected using Real-time PCR. SHEDs served as the blank control group, SHEDs/HA/TCP served as the negative control group, and SHEDs/hTDM and SHEDs/pTDM served as the experimental groups. RNAiso Plus (Takara Biomedical Technology, Beijing, China), PrimeScript™ RT reagent (Takara Biomedical Technology, Beijing, China), and SYBR Premix (QIAGEN, Hilden, Germany) were used to extract total RNA, reverse transcribe RNA to cDNA, and detect the related genes’ expression levels (DSPP, POSTN, TGF-β1, ALP, COL-1, OCN, and RUNX2). According to the instructions, the configuration of each 10 μL PCR reaction solution contained 5 μL SYBR Premix, 0.4 μL PCR forward primer, 0.4 μL PCR reverse primer, 1 μL DNA template, and 3.2 μL sterile water. After normalization to the GAPDH internal reference gene, relative mRNA expression was determined using the 2−ΔΔCT method. Supplemental Table 1 displays Real-time PCR primer sequences. The experiment was repeated at least three times using biological samples and technical means.
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3

Quantitative Real-Time PCR Protocol

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For qRT-PCR, total RNA was prepared using the TRIzol reagent (Tel-Test, Inc., USA), and cDNA was synthesized using the SuperScript pre-amplification system (Invitrogen). The PCR primers and cycling conditions are described in the Xenopus Molecular Marker Resource (University of Texas). Additional primers are described in Table 2. The PCR reactions were performed with SYBR Premix (Qiagen, USA) and a thermal cycler real-time system (Qiagen Rotor-Gene-Q, USA).
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4

Molecular Regulation of Smooth Muscle Differentiation

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Glucose, mannitol, antibodies against myocardin, SM α-actin and α-tublin, antibiotics and ERK inhibitor PD98059 were purchased from Sigma-Aldrich (St. Louis, MO). The phospho-p44/42 (ERK) MAPK (Thr202/Tyr204) and total p44/42 (ERK) MAPK antibodies were purchased from Cell Signaling (Beverly, MA). The horseradish peroxidase (HRP)-conjugated secondary antibodies, DMEM low Glucose medium and fetal bovine serum (FBS) were from Hyclone Laboratories (Logan, Utah). Reagents for reverse transcription, SYBR Premix, Ex Taq and primers were purchased from Qiagen (Valencia, CA). Primers for quantitative PCR and RT-PCR are as following: myocardin, 5′-CAGAAAGTGACAAGAACGATACAG-3′ (forward), 5′-TGAAGCAGCCGAGCATAGG-3′ (reverse) [24 (link)], SM α-actin, 5′-CGGGCTT TGCTGGTGATG-3′ (forward), 5′-GGTCAGGATCCCTCTCTTGCT -3′ (reverse) [25 (link)], β-actin 5′-CGTGGGCCGCC CTAGGCACCA -3′ (forward), 5′-TTGGCCTTA GGGTTCAGGGGG-3′ (reverse) [26 (link)].
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5

Stem Cell Transcriptional Profiling

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ASCs, DFCs, and SHEDs at passages 1, 3, 5, and 7 were harvested for extraction of total RNA using RNAiso Plus (Takara Biomedical Technology, Beijing, China) according to the manufacturer’s protocol. Prime-Script™ RT reagent kit (Takara Biomedical Technology, Beijing, China) was used to reverse transcribe the RNA into cDNA. Quantitative real-time PCR (RT-qPCR) was performed using SYBR Premix (QIAGEN, Hilden, Germany) to quantify the expression levels of Nanog, Sox2, PDGFRα, and β-III tubulin. At least three technical and biological replicates were performed.
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6

Profiling Cellular miRNA via qRT-PCR

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Total RNA was isolated from cells using TRIzol reagent (QIAGEN), and cDNA was obtained using an Omniscript RT kit (QIAGEN) under the guide of the manufacturer’s instructions. qRT-PCR was performed with SYBR Premix (QIAGEN) on the BIO-RAD system (BIO-RAD-96CFX) following the standard procedure. Stem-loop RT primers (QIAGEN) were used to quantify the expression of miRNA, and the expression of GAPDH was used as a reference. The specific protocol was based on the manufacturer’s instructions, and miRNA primers were synthesized by RiboBio. The results were analyzed by the 2–ΔΔCt method.
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7

Quantifying miRNA Expression using qRT-PCR

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Total RNA was isolated from cells using TRIzol reagent (QIAGEN), and cDNA was obtained using Omniscript RT kit (QIAGEN) according to the manufacturer’s instructions. qRT-PCR was performed with SYBR Premix (QIAGEN) on the BIO-RAD system (BIO-RAD-96CFX) according to standard methods. Stem-loop RT primers (QIAGEN) were used to quantify the expression of miRNA, and the expression of U6 was used for standardization. The specific method was based on the manufacturer’s instruction, and miRNA primers were ordered from Ribobio. The results were analyzed by the 2-△△Ct method.
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