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Pcr primers

Manufactured by RiboBio
Sourced in China

PCR primers are short, synthetic DNA sequences used in the polymerase chain reaction (PCR) to amplify specific target DNA sequences. They act as the starting point for DNA synthesis, initiating the replication process. PCR primers are designed to be complementary to the target DNA region, allowing the DNA polymerase enzyme to replicate the desired sequence.

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11 protocols using pcr primers

1

Gene Expression Analysis by RT-qPCR

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The expression of the genes to be studied in the cells was detected using RT-qPCR. The TRIzol reagent was utilized in order to get total RNA from the cultured cells (Invitrogen, Carlsbad, USA). SYBR Green (Qiagen) was used for the qPCR amplification process after a cDNA kit (Applied Biosytems) was used to produce reverse transcription of RNA (1000 ng) into cDNA. The other relative genes expression in some experiments were determine by the 2−ΔΔCT method [31 (link)]. The PCR primers (RiboBio, Guangzhou, China) are as follows. miR-26b: Forward, 5′-CCGGGACCCAGTTCAAGTAA-3′, Reverse, 5′-CCCCGAGCCAAGTAATGGAG-3′, CEP-135: Forward, 5′-CGTCCCTCCGCGCCATTTTCA-3′, Reverse, 5′-CGGTATCCCAGCTGATCCAGCCTT-3′, GAPDH Forward, 5′-AGAAGGCTGGGGCTCATTTG-3′, Reverse, 5′-AGGGGCCATCCACAGTCTTC-3′
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2

miR-4516 Expression in A549 Cells

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A549 cells were seeded in 10 cm culture dishes treated with 50, 100, 250, or 500 μg/mL PM2.5 for 24 h. Total RNA was isolated according to the instructions provided by the manufacturer of TRIZOL. The total RNA from human serum was extracted using miRNeasy Serum/Plasma Kit (Qiagen, 217184, Germany). The expression levels of miR-4516 were amplified with PCR primers (RiboBio, China) on a Quant Studio 6 Flex system (Applied Biosystems, Life Technologies, USA). The relative expression levels of miRNAs were normalized against U6 and were calculated using the 2−ΔΔCt method. All of the experiments were performed in triplicates.
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3

RNA Extraction and RT-qPCR Analysis

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Total RNA was extracted from tissues with TRIzol Reagent (TaKaRa, Japan) according to the manufacturer’s protocol. The isolated RNA was then transcribed into cDNA using a reverse transcription kit (TaKaRa, Japan). RT-qPCR was performed to quantify the RNA expression using the standard protocol with an SYBR Green PCR kit (Roche, USA) on the StepOne plus RT-qPCR System (ABI, USA). All PCR primers were purchased from RiboBio Co., Ltd. (Guangzhou, China) (primer list in Supplementary Table S1). The PCR thermocycling program was as follows: 95°C for 30 s followed by 40 cycles of 95°C for 5 s and 60°C for 30 s. Each sample was analyzed in triplicate, and the relative expression was calculated using the 2−ΔΔCt method relative to that of GAPDH.
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4

Isolation and Analysis of Cellular and Exosomal RNA

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The total RNA was extracted by SunShine Bio™ kit (SunShine Bio Co., Ltd., Nanjing, China). The total RNAs of the cells and the exosomes were extracted by Trizol (Invitrogen, Carlsbad, CA, USA). The concentration and purity of RNA (the ratio of A260/A280) were evaluated on NANODROP 2000C (Thermo Fisher Scientific Co., Ltd., MA, USA), the ratio of RNA purity at 1.8–2.0 was eligible. The primers of miR-205 and U6 as well as PCR primers were all purchased from Guangzhou RiboBio Co., Ltd. (Guangdong, China), the primer sequence was not provided for business factors. The reverse transcription of VEGFA and β-actin was conducted by MMLV kit (Invitrogen, Carlsbad, CA, USA), PCR primers were synthetized by the Shanghai branch of Invitrogen (Shanghai, China). VEGFA primers are as follows: Forward: 5′-ACGGATCCATGGCGGTCCCACGTC-3′, Reverse: 5′-TTGAATTCTTACCGCCTCGGCTTGTCAC-3′. β-actin primer are as follows: Forward: 5′-ATCCGCAAAGACCTGT-3′, Reverse: 5′-GGGTGTAACGCAACTAAG-3′. The data were analyzed using 2−ΔΔCt method.
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5

Apoptotic Pathway Gene Expression Analysis in HepG2 Cells

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RT-qPCR was used to evaluate the expression levels of the key apoptotic genes, BCL2 and BAX, and AP-1 downstream gene ETS1. After phosphate-buffered saline (PBS) or veratramine treatment for 48 h, HepG2 cells were subjected to total RNA isolation using TRIzol® reagent. Subsequently, cDNA was synthesized using the HiScript III 1st Strand cDNA Synthesis kit and qPCR was performed using the ChamQ SYBR qPCR Master Mix according to the manufacturer's instructions. Thermocycling parameters were optimized as 5 min at 95°C, followed by 40 cycles at 95°C (15 sec), 60°C (30 sec); melt curve: 95°C (15 sec), 60°C (30 sec) and 95°C (15 sec). PCR primers were provided by Guangzhou RiboBio Co., Ltd., and β-actin was used as the internal reference. Quantitative analysis of relative mRNA expression levels was performed according to the 2−ΔΔCq method (36 (link)). Primer sequences were as follows: BCL2 forward, 5′GTGGAGGAGCTCTTCAGGGA3′ and reverse, 5′AGGCACCCAGGGTGATGCAA3′); BAX forward, 5′GGCCCACCAGCTCTGAGCAGA3′ and reverse, 5′GCCACGTGGGCGTCCCAAAGT3′; ETS1 forward, 5′GCGCGCTAGCAACTTGCTACCATCCCGT3′ and reverse, 5′GCGCAAGCTTTGCCATCACTCGTCGGC3′; β-actin forward, 5′ACAAAGTGGTCATTGAGGGC3′and reverse, 5′GCCGTCAGGCAGCTCGTAGC3′.
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6

Quantitative Analysis of miRNA and EMT Markers

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Total RNA from tissues and cells were extracted using the TRIZOL reagent (Invitrogen) and reverse transcribed by using the M-MLV RT kit (Promega). For the detection of mature miR-338-3p, specific RT primers and PCR primers (Ribobio) were constructed, and cDNA was amplified using SYBR® Green PCR Master Mix (Toyobo, Osaka, Japan). The relative transcript levels of E-cadherin, N-cadherin, fibronectin, vimentin and ZEB2 were detected using SYBR® Green qPCR SuperMix (Invitrogen). The primers sequences are listed in the Supplementary Table 2. Relative expression was normalized to snRNA U6 or β-actin and calculated using the 2−ΔΔCt method.
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7

Quantifying miR-27a Expression in Tissues

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Total RNA from the tissue sample was extracted using Trizol RNA isolation reagent (Invitrogen) according to the manufacturer's protocol. The expression levels of miR‐27a were amplified with PCR primers (RiboBio) on the ABI 7900HT Real‐Time PCR System (Applied Biosystems). Real‐time PCR was performed with Power SYBR Green PCR Master Mix (Applied Biosystems Inc). All real‐time reactions were performed in triplicate.
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8

Evaluating miRNA Expression in A549 Cells Exposed to PM2.5

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A549 cells seeded in 10 cm culture dishes were treated with 50, 100, 250, or 500 μg/mL PM2.5 for 24 h. Total RNA was isolated from cell lysates, according to the instructions provided by the manufacturer of TRIZOL (Invitrogen, USA). The total RNA from animal and human serum was extracted using TRIZOL reagent (Invitrogen, USA) and the miRNeasy Serum/Plasma Kit (Qiagen, Germany), respectively.
A total of 1 μg RNA was converted to cDNA using a One Step PrimeScript® miRNA cDNA Synthesis Kit (Takara, Shiga, Japan). The expression levels of miR-802, −1322, −1469, −4319, −933, and −3176 were amplified with PCR primers (RiboBio, China) on a Quant Studio 6 Flex system (Applied Biosystems, Life Technologies, USA). The relative expression levels of miRNAs were normalized against U6, and were calculated using the 2-ΔΔCt method. All of the experiments were performed in triplicates.
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9

Quantifying miR-183 and PDCD4 Expressions

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Total RNA was extracted from the cultured cells using Trizol reagent (Life Technologies, USA) according to the manufacturer’s protocol. For miR-183 expression level detection, total RNA was reverse-transcribed with a miR-183-specific RT primer (RiboBio, China) and amplified with PCR primers (RiboBio, China) on the ABI 7300 Real-Time PCR System (Life Technologies, USA). The relative expression of miR-183 was normalized against U6. Real-time RT-PCR for PDCD4 was performed with primers specific for PDCD4 (forward, 5′-TATGATGTGGAGGAGGTGGATGTGA-3′; and reverse, 5′-CCTTTCATCCAAAGGCAAAACTACAC-3′) (Frankel et al., 2008 (link)), and the relative expression level was normalized against β-actin (forward, 5′-ATCCGCAAAGACCTGT-3′; and reverse, 5′-GGGTGTAACACTAAG-3′), which was designed by Invitrogen (Life Technologies, USA). The difference between miR-183 and PDCD4 expressions in cells treated with mimic/inhibitor and each NC was calculated using the 2−ΔΔCt method (Livak and Schmittgen, 2001 (link)), where ΔCt = (CtmiR-183/PDCD4 - Ctu6/β-actin) and ΔΔCt = ΔCtmimic/ihibitor -ΔCtNC.
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10

Quantitative analysis of miRNA and mRNA

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The total RNAs were extracted by Trizol (Invitrogen Inc., Carlsbad, CA, USA), and the RNA concentration and purity were evaluated. As to miR-576-5p and U6, the PCR primers and Stem-loop specific reversely transcribed primers were acquired from Guangzhou RiboBio Co., Ltd. (Guangdong, China). Primer sequences were not provided here due to business factors. Random primers with MMLV reverse transcriptase (Invitrogen) were selected for the reverse transcription of ANXA2, Bcl-2 and Bax by glyceraldehyde phosphate dehydrogenase (GAPDH). The PCR primers were synthesized by Invitrogen. PCR reaction was performed using a SYBR Green PCR Master Mix (BioTeke Co., Ltd., Beijing, China) with U6 and GAPDH as the internal reference. The data were analyzed using the 2−ΔΔCt method [22 (link)].
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