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5 protocols using sybr green premix dimereraser

1

Quantitative RT-PCR for Gene Expression

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RNAiso Plus (Takara, Otsu, Japan) was used to isolate mRNA from cells or tissue.
The PrimeScript RT Master Mix (Takara, Otsu, Japan) was used to generate cDNA.
qPCR was performed using a SYBR Green Premix DimerEraser (Takara, Otsu, Japan)
on the 7900HT Fast Real-Time PCR system (Applied Biosystems). All reactions had
a melting curve with a single peak. The cycle threshold (CT) values for the
triplicate samples were averaged and the data were analyzed using the
ΔΔCT method, where fold
change = 2−ΔΔCT.
All data analyzed were normalized to beta-Actin or GAPDH expression. For the
specific primer sequences (Sangon Biotech, Shanghai, China), see Supplementary Table S4.
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2

Validation of Differentially Expressed circRNAs in TSCC

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According to the Log2FC absolute value, the top five upregulated and downregulated DEcircRNAs were selected as candidate DEcircRNAs for further investigation. RT-qPCR was performed to determine the relative expression levels of 10 candidate circRNAs in tumor and paired Ctrl tissues derived from 60 patients with TSCC. Briefly, total RNA was extracted using TRIzol® reagent (Invitrogen; Thermo Fisher Scientific, Inc.). The detection of circRNAs was performed following digestion of the linear RNA using RNase R (Epicentre; Illumina, Inc.). Subsequently, the synthesis of cDNA was carried out (denaturation at 65°C for 5 min, reverse transcription at 42°C for 18 min and inactivation at 98°C for 5 min) using the PrimeScript™ RT reagent kit (Takara Bio, Inc.), followed by its amplification using SYBR-Green Premix DimerEraser™ (Takara Bio, Inc.). Lastly, the relative expression levels of the circRNAs were calculated using the 2-ΔΔCq method (16 (link)). The thermocycling conditions for qPCR were as follows: Pre-denaturation at 95°C for 3 min; followed by 40 cycles of denaturation at 95°C for 15 sec and annealing/elongation at 61°C for 20 sec. GAPDH was used as an internal reference for circRNAs. The primers are shown in Table SI.
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3

Glutamine Modulates IL6R and CXCR4 in Pancreatic Cancer

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Pancreatic cancer cells SW1990, BxPC-3, CaPan-2 and SU.8686 were cultured in media with different concentrations of glutamine (0 and 2 mM). RT-qPCR was performed to evaluate the relative expression levels of
IL6R and
CXCR4. Total RNA was isolated from cell lines using the EZ-press RNA Purification kit (EZBioscience, Shanghai, China), followed by cDNA synthesis using a Color Reverse Transcription kit (EZBioscience). The reverse transcription of RNA into cDNA was performed according to the manufacturer’s protocol. The product were amplified using SYBR-Green Premix DimerEraser (Takara, Dalian, China) on theLightCycler480 II system (Roche, Basel, Switzerland). The relative expression was determined using the 2
‒ΔΔCq method. qPCR was performed under the following conditions: initial denaturation at 95°C for 3 min followed by 40 cycles of 95°C for 30 s, 60°C for 30 s and 72°C for 30 s, with a final extension at 72°C for 1 min.
β-Actin was selected as an internal reference, to compare gene expression in different samples. The following primers were used:
IL6R (forward: 5′-GGCTCTGAAGGAAGGCAAGA-3′, reverse: 5′-CTGGCATCTGGTCGGTTGT-3′);
CXCR4 (forward: 5′-CAGTGAGGCAGATGACAG-3′, reverse: 5′-ACAATACCAGGCAGGATAAG-3′); and
β-actin (forward: 5′-CGTGCGTGACATTAAGGAAGAGT-3′, reverse: 5′-GGAAGGAAGGCTGGAAGAGT-3′).
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4

Quantification of Bcl-2 Expression in NIT-1 Cells

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NIT-1 cells were seeded at 4 × 105 cells/well in 6-well plates and treated with a combination of IFN-γ and TNF-α for indicated times. Total RNA was extracted using Trizol (Roche) and then reverse transcribed into cDNA by using RT kit (TOYOBO). Quantitative PCR with SYBR Green Premix DimerEraser (Takara) was performed using an ABI 7000 sequence detection system and mRNA levels were normalized according to levels of the housekeeping gene GAPDH. Primer sequences for both quantitative PCR amplification were as follows: Bcl-2 forward, 5′-GTACCTGAACCGGCATCTG-3'; Bcl-2 reverse, 5′-GGGGCCATATAGTTCCACAA-3′. GAPDH forward, 5′-ACCACAGTCCATGCCATCAC-3′; GAPDH reverse, 5′-TCCACCACCCTGTTGCTGTA-3′.
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5

Quantifying mRNA Expression by qRT-PCR

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TRIzol reagent (Roche Diagnostics) was used to extract total RNA, which was then reverse transcribed into cDNA using the RT kit (FSQ-101, Toyobo Co., Ltd.). The product was processed with SYBR-Green Premix Dimer Eraser (Takara Biotechnology Co., Ltd.), and the level of mRNA was then measured using the ABI 7000 sequence detection system (ABI PRISM® 7000, Thermo Fisher Scientific, Inc.) (1 cycle, 95°C, 15 min; 40 cycles, 95°C, 10 sec, 60°C, 32 sec). GAPDH was used as the housekeeping gene for normalization. The primers and sequences used were as follows: IL-1β forward, 5′-CGA TCA CTG AAC TGC ACG CT-3′ and reverse, 5′-AGA ACA CCA CTT GTT GCT CCA-3′; GAPDH forward, 5′-AAGATC AAG ATC ATT GCT CCT CCT G-3′ and reverse, 5′-GCC GGA CTC GTC ATA CTC CT-3′; and PCSK9 forward, 5′-ACG ATG CCT GCC TCT ACT CC-3 and reverse, 5′-GCC TGT GAT GTC CCA CTC TGT-3′.
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