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16 protocols using trizol reagent

1

RNA Extraction and RT-qPCR Analysis

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Trizol reagent (ELK Biotechnology, Wuhan, China) was used to extract the RNA from cells. RNA was reversed transcribed into cDNA using an EntiLink™ 1st Strand cDNA Synthesis Kit (ELK Biotechnology). Next, RT-qPCR was performed using the EnTurbo™ SYBR Green PCR SuperMix (ELK Biotechnology, EQ001) on the StepOne™ Real-Time PCR (Life technologies, Carlsbad, California, USA). The primers were as follows: H-ACTIN, forward, 5′-GTCCACCGCAAATGCTTCTA-3′, reverse, 5′-TGCTGTCACCTTCACCGTTC-3′; H-LOC100129516, forward, 5′-GCTGTGGTTATCCAATCCCTC-3′, reverse, 5′-GGCAAATGACTTCACCTCCC-3′; H-lnc-KCNC3-3:1, forward, 5′-GAAGATTGGGAACCGACAACA-3′, reverse, 5′-TTGCATCGAGAATCGTGCTC-3′; ENSG00000236780.1, forward, 5′-GATGCTCTCCACACCAGTCCA-3′, reverse, 5′-TGTGAACAGGGCTGGAATGAG-3′; ENSG00000205959.3, forward, 5′-GCTGTCCGAGCAAATGTCTCT-3′, reverse, 5′-GTGGCACTGCTGAGAAGAGGA-3′; ENSG00000261482.1, forward, 5′-GGGCTGCTGACTTCCACAG-3′, reverse, 5′-AATATCCACTCTGGGTGCAGC-3′. β-actin acted as the inner control. The 2−ΔΔCT method was used for data analysis.
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2

Cardiac Gene Expression Analysis

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Total RNA was extracted from the heart tissues using the TRIzol reagent (ELK Biotechnology) following the manufacturer’s instructions. Then, RNA samples (2µg) were reverse transcribed into cDNA using the EntiLink 1st Strand cDNA Synthesis Super Mix (ELK Biotechnology, EQ031). Then, qRT-PCR was performed in the QuantStudio 6 Flex System (Life Technologies) with the cDNA samples using the EnTurbo SYBR Green PCR SuperMix (ELK Biotechnology, EQ001). Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) was used as the internal control. The qPCR primers (Table 1) were designed and synthesized by HY cell biotechnology (Wuhan, China). The relative gene expression levels were analyzed using the 2−ΔΔCt method.
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3

Quantitative Gene Expression Analysis

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RNA was isolated from cells using Trizol reagent (ELK Biotechnology, China) according to the manufacturer's protocol. 1 μg of RNA was used to synthesise cDNA by cDNA Synthesis Kit (TOYOBO, Japan). cDNA was subsequently used for real-time fluorescence quantitative PCR (qPCR) using the ABI QuantStudio™6 Flex System (USA) and the Real-time fluorescence quantitative PCR (qPCR) was subsequently performed using ABI QuantStudio™6 Flex System (USA) and UltraSYBR Mixture (CWBIO, China). Gene primers: SLC12A2 (Forward 5′-CCTCTACACAAGCCCTGACTTAC-3′ and Reverse 5′-CGTGAGTTTGGAGCACCTGTCA-3′); GAPDH (Forward 5′-GTCTCCTCTGACTTCAACAGCG-3′ and Reverse 5′-ACCACCCTGTTGCTGTAGCCAA-3′). The relative mRNA expression levels were calculated using the 2-△△Ct method.
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4

Quantifying miRNA-181b-5p Expression

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Total RNA was isolated from cells using the Trizol reagent (ELK Biotechnology, Wuhan, China). Next, RNA samples were reversed transcribed into cDNA using an EntiLink™ 1st-Strand cDNA Synthesis Kit (ELK Biotechnology). Then, RT-qPCR was carried out using the EnTurbo™ SYBR Green PCR SuperMix (ELK Biotechnology) on the StepOne™ Real-Time PCR System (Thermo Fisher Scientific). The 2−ΔΔCT method was used for data analysis. The U6 gene worked as an internal control. The primers were as follows: U6, forward, 5′-CTCGCTTCGGCAGCACAT-3′, reverse, 5′-AACGCTTCACGAATTTGCGT-3′; hsa-miR-181b-5p, forward, 5′-TCGGTGGGTCTCAACTGAATT-3′, reverse, 5′-CTCAACTGGTGTCGTGGAGTC-3′. PDHX, forward, 5′-AAGATTACCGAC TCCAGACCAA-3′, reverse: 5′-TGTCCAGGAGTTGATACTGCTG-3′. Actin, forward, 5′-GTCCACCGCAAATGCTTCTA-3′, reverse: 5′-TGCTGTCACCTTCACCGTTC-3′.
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5

Quantitative Analysis of miRNA Expression in HUVECs

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TRIzol® reagent (ELK Biotechnology, Co., Ltd., Wuhan, China) was used to extract total RNA from HUVECs, and an EntiLink™ 1st strand cDNA Synthesis Kit (ELK Biotechnology, Co., Ltd.) was then used to synthesize cDNA. Next, RT-qPCR was performed on a StepOne™ Real-Time PCR System. The 2-DDCq method was used to quantify the data. The primers used in the present study were purchased from Shanghai GenePharma Co., Ltd. (Shanghai, China), and their sequences are as follows: U6 forward, 5’-CTCGCTTCGGCAGCACA- 3’, reverse, 5’-AACGCTTCACGAATTTGCGT-3’; β-actin forward, 5’-GTCCACCGCAAATGCTTCTA-3’, reverse, 5’-TGCTGTCACCTTCACCGTTC-3’; miR-342-5p, 5’-AGGGGTGCTATCTGTGATTGA- 3’; miR-485-3p forward, 5’-GGCCGTCATACACGGCTC- 3’, reverse, 5’-CTCAACTGGTGTCGTGGAGTC- 3’; miR-26a-5p forward, 5’-UCCAUAAAGUAGGAAACACUACA- 3’, reverse, 5’-CAGUACUUUUGUGUAGUACAA- 3’; and BID forward, 5’-AAGAAGGTGGCCAGTCACAC-3’, reverse, 5’-GTCCATCCCATTTCTGGCTA-3’.
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6

Quantifying lncRNA PCAT6 Expression

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Total RNAs from BEAS-2B, A549, NCI-H1299, NCI-H1975, or exosomes derived from A549 were extracted using Trizol reagent (ELK Biotechnology, Wuhan, China). Next, total RNAs was reversely transcribed into corresponding cDNA through EntiLink™ 1st Strand cDNA Synthesis Kit (ELK Biotechnology). After that, the StepOne™ Real-Time PCR System (Thermo Fisher Scientific, Waltham, MA, USA) was applied to perform RT-qPCR. The primers were listed as follows: β-actin, forward, 5’-GTCCACCGCAAATGCTTCTA-3’, reverse, 5’-TGCTGTCACCTTCACCGTTC-3’; KLF1, forward, 5’-AGGATGACTTCCTCAAGTGGTG-3’, reverse, 5’-GAGAAGTTGGTGAGGAGGAGATC-3’; PCAT6, forward, 5’-TCCAACTCCCAGACCTCACG-3’, reverse, 5’-GAGGAGCGCCTCATCACCAG-3’. The method of 2−ΔΔCT was applied to calculate the expression of lncRNA PCAT6 according to the previous literature [36 (link)]. β-actin was viewed as an internal control.
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7

Transcriptomic Analysis of Tissue Samples

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Total RNA was isolated from tissues using the Trizol reagent (ELK Biotechnology, Wuhan, China). Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) was used to qualify the concentration of RNAs. Affymetrix Expression Console Software was used for microarray analysis. DESeq2 was used for differentially expressed gene analysis (15 (link)). DEGs were identified with p ≤ 0.05 and AveExpr ≥ 3.
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8

RNA Isolation and Real-Time qPCR Analysis

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Total RNA was isolated using the TRIzol reagent (ELK Biotechnology, Wuhan, China) according to the manufacturer’s protocol. cDNA was synthesized using the EntiLink™ 1st Strand cDNA Synthesis Kit. All real-time polymerase chain reactions (PCRs) were performed using EnTurbo™ SYBR Green PCR SuperMix Kit on a StepOne™ Real-Time PCR system (Life Technologies, New York, NY, USA). GAPDH was used as an internal control for normalization of the relative expression levels. Gene expression levels were calculated using the 2–ΔΔCT method relative to that of the internal control. Primers are listed in Table 3.
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9

Brain RNA Extraction and Gene Expression

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Total RNA was extracted from brain tissue using TRIzol reagent (ELK Biotechnology, China) according to the manufacturer’s instructions. RNA concentrations were equalized and converted to cDNA using the EntiLink™ 1st Strand cDNA Synthesis Kit (ELK Biotechnology, China). Gene expression was measured using a StepOne™ Real-Time PCR system. The sequences of primers used in these experiments were listed in the Supplementary material.
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10

Quantifying mRNA Levels in HUVECs

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Total RNA was extracted from HUVECs using a TRIzol® reagent (ELK Biotechnology, Co., Ltd.) according to the manufacturer's instructions. Subsequently, total RNA was reverse transcribed into complementary DNA (cDNA) using the EntiLink™ 1st Strand cDNA Synthesis Kit (ELK Biotechnology, Co., Ltd.). qPCR was performed using the EnTurbo™ SYBR Green PCR SuperMix kit (ELK Biotechnology, Co., Ltd.) on the StepOne™ Real-Time PCR system (Thermo Fisher Scientific, Inc.). The thermocycling conditions were used as follows: 3 min at 95°C, followed by 40 cycles of 10 s at 95°C, 30 s at 58°C, and 30 s at 72°C. The primer sequences used were as follows: For β-actin, forward, 5′-GTCCACCGCAAATGCTTCTA-3′, and reverse, 5′-TGCTGTCACCTTCACCGTTC-3′; for LINC00452, forward, 5′-GTCCACTGTGAAGCTCGACG-3′, and reverse, 5′-GAGCACCACTCTGTCCACTCAG-3′; and for IGF1R, forward, 5′-GCATCATCATAACCTGGCACC-3′, and reverse, 5′-GTAAACGGCGTACTGAGTCCAG-3′. The RT-qPCR results were calculated using the 2−ΔΔCq method (25 (link)), and β-actin was used as the internal control for normalization.
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