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Specific primers

Manufactured by Sangon
Sourced in China, Japan

Specific primers are short DNA sequences used in various molecular biology techniques to selectively amplify targeted genetic regions. They serve as the starting point for DNA synthesis during processes such as polymerase chain reaction (PCR).

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52 protocols using specific primers

1

Isolation and Analysis of circRNA

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Tissues or cells were lysed in Trizol reagent (Solarbio) for the isolation of total RNA. For extraction of circRNA, the RNA was further treated by RNase R (Geneseed, Guangzhou, China). The complementary DNA (cDNA) was generated by reverse transcription using the First‐Strand cDNA Synthesis kit (Yeasen, Shanghai, China) and then used for qRT‐PCR assay after the mixture with SYBR (Thermo Fisher) and specific primers (Sangon, Shanghai, China). The primers were listed as: circCDR1as (Forward, 5′‐CCCAGTCTTCCATCAACTGG‐3′; Reverse, 5′‐ACCTTGACACAGGTGCCATC‐3′), SOX5 (Forward, 5′‐AGGTTTGGACTCACTTGACAGG‐3′; Reverse, 5′‐GTGAGGCTTGTTGGGAAAACTC‐3′) and miR‐219a‐5p (Forward, 5′‐TCTACAGTGCACGTGTCTCCAGT‐3′; Reverse, 5′‐CTCTCATTTGCTATATTCA‐3′). The glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH) (Forward, 5′‐CAGCCTCAAGATCATCAGCA‐3′; Reverse, 5′‐GTCTTCTGGGTGGCAGTGAT‐3′) and U6 (Forward, 5′‐CTCGCTTCGGCAGCACA‐3′; Reverse, 5′‐AACGCTTCACGAATTTGCGT‐3′) were regarded as internal controls. The 2−ΔΔCt method was used to calculate the relative gene expression level.24
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2

RNA Isolation and qRT-PCR Analysis

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Total RNA was isolated with TRIzol regent (Life Technology, Carlsbad, CA, USA). The expression of mRNA level was analyzed by qRT-PCR analysis as described previously (Wang et al., 2015 (link)). Specific primers were synthesized by Sangon Biotech (Shanghai, China), and the sequences were described as follows:
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3

Circular RNA Quantification Protocol

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Tissues or cells were lysed using Trizol reagent (Thermo Fisher) and were used for RNA extraction. For circRNA extraction, the obtained RNA was further incubated with RNase R (GeneSeed, Guangzhou, China) following instructions of manufacturer. The RNA was reversely transcribed to cDNA with specific reverse transcription kit (Thermo Fisher). The cDNA together with SYBR Green (Solarbio, Beijing, China) and specific primers (Sangon, Shanghai, China) was used for qRT-PCR. The primers included: circ_0000517 (sense, 5′-GGGAGGTGAGTTCCCAGAG-3′; antisense, 5′-CAGGGAGAGCCCTGTTAGG-3′), IGF1R (sense, 5′-AGTATGGAGGGGCCAAGCTA-3′; antisense, 5′-CTTTTGGCCTGGACATAGAAGA-3′), miR-326 (sense, 5′-CATCTGTCTGTTGGGCTGGA-3′; antisense, 5′-AGGAAGGGCCCAGAGGCG-3′), U6 (sense, 5′-CTCGCTTCGGCAGCACA-3′; antisense, AACGCTTCACGAATTTGCGT), and GAPDH (sense, 5′-CATGAGAAGTATGACAACAGCCT-3′; antisense, 5′-AGTCCTTCCACGATACCAAAGT-3′). GAPDH or U6 was used as reference. Relative RNA level was calculated through 2−ΔΔCt method [17 (link)].
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4

Trigeminal Nucleus Caudalis Gene Expression

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Rats were sacrificed under chloral hydrate anesthesia. The trigeminal
nucleus caudalis (TNC), 1 to 5 mm from the obex, according to the
atlas by Paxinos and Watson,30 was rapidly separated and used for further analysis.31 (link) Total RNA was extracted from TNC segments using the RNAiso Plus
reagent (Takara) following the manufacturer’s instructions. Next, cDNA
was synthesized using the PrimeScript™ RT reagent kit (Takara, Tokyo,
Japan). RT-PCR was performed on a CFX96 Touch thermocycler (Bio-Rad)
using the SYBR® Premix Ex Taq™ II (Takara). The following specific
primers (Sangon Biotech, Shanghai, China) were used as follows:
P2X4R_forward: 5′-TCG TGT GGG AAA AGG GCT AC-3′, P2X4R_reverse: 5′-GTC
TGG TTC ACG GTG ACG AT-3′; GAPDH_forward: ATG ACT CTA CCC ACG GCA AGC
T-3′, GAPDH_reverse: 5′-GGA TGC AGG GAT GAT GTT CT-3′. Relative gene
expression was normalized to the internal reference GAPDH using the
2–ΔΔCTmethod.
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5

Quantification of miR-212 and CASP8 Expression

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RNA was extracted with TRIzol reagent (Thermo Fisher) using the acid guanidinium thiocyanate-phenol-chloroform method [25] . RNA (500 ng) was reverse transcribed to cDNA using a specific reverse transcription kit (iGene Biotechnology, Guangzhou, China). The cDNA was mixed with SYBR (Thermo Fisher) and specific primers (Sangon, Shanghai, China), and then the mixture was used for qRT-PCR under the following conditions: 95 °C for 5 min, 40 cycles of 95 °C for 20 s, and 60 °C for 1 min. The primers are shown in Table 1. U6 or β-actin was used as a reference for miR-212 and CASP8. The relative RNA expression was tested with the 2 -ΔΔCt method [26] .
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6

Quantification of NALCN mRNA Expression

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NALCN mRNA was measured by qRT-PCR. The retrotrapezoid nucleus area was dissected under a microscope. Total RNAs was extracted using the Eastep® Super RNA extraction kit (Promega, Shanghai, China). cDNA was synthesized with a GoScript™ Reverse Transcription Kit (Promega, Shanghai, China). Then, the cDNA was used as a template to quantify the NALCN expression level using GoTaq® qPCR Master Mix (Promega, Shanghai, China) and specific primers (Sangon Biotech, Shanghai, China) according to the manufacturer’s protocol. The forward and reverse primers of NALCN were: (5’−3’) GTCCTGACGAATCTCTGTCAGA and CTGAGATGACGCTGATGATGG, respectively. The GAPDH gene was used as an internal control. The PCR conditions were as follows: 3 min at 95°C; 40 cycles: 15 s, 95°C; 30 s, 55°C; 30 s, 72°C.
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7

Quantifying Hepatic Oxidative Stress Markers

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Txnrd1, Txnrd3, Txn1, Txn2, Nrf2, keap1, and p65 transcript expression levels in the liver tissue were detected by real-time fluorescent quantitative PCR (Applied Biosystems, Foster City, CA, USA). RNA was extracted from liver tissue according to the manufacturer’s instructions, and the TAKARA reverse transcription kit-RR047A was used to obtain complementary DNA (cDNA). The reverse-transcribed cDNA was used as a template, β-actin acted as an internal reference gene, and specific primers (Sangon Biotech, Shanghai, China) of the target genes were synthesised according to the sequences in Table 1. A fluorescence quantitative PCR amplification system (cDNA template: 1 μL, Primer F: 0.5 μL, Primer R: 0.5 μL, TB Green: 7.6 μL, Rox: 0.4 μL (Takara Biomedical Technology Co., Ltd, Beijing, China), ddH2O: 10 μL). The PCR conditions were as follows: 5 min at 95 °C, 40 cycles of 10 s at 95 °C, 30 s at 60 °C, and 30 s at 72 °C followed by a melting curve step. The mRNA expression level was calculated using the 2−△△CT method and the data were analysed.
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8

Total RNA Extraction from Glioma Cells

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For total RNA extraction from human glioma tissues and SHG‐44, U251, A172 and NHA cells, collected tissues and cells were lysed in TRIzol reagent (Invitrogen, Carlsbad, CA, USA). A Reverse Transcription Kit (Takara, Otsu, Japan) and specific primers (Sangon Biotech, Shanghai, China) were used for reverse transcription of the separated total RNA. The individual primers sequences are mentioned in Table 1.
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9

Quantitative Analysis of HULC, miR-200a-3p, and ZEB1

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Total RNA was extracted by RNAiso Plus (Takara, Dalian, China). The reaction mixture (20 μl) containing 1 μg of total RNA was reversely transcribed to cDNA by using PrimeScript RT-polymerase (Takara, Dalian, China). Quantitative PCR was performed on the cDNA using specific primers (Sangon, Shanghai, China) for HULC (F:5‘-TCATGATGGAATTGGAGCCTT-3′, R: 5′-CTCTTCCTGGCTTGCAGATTG-3′), miR-200a-3p (5′- AACACTGTCTGGTAACGATGTCGT-3′), ZEB1 (F: 5′- CAGCTTGATACCTGTGAATGGG-3′, R: 5′-TATCTGTGGTGTGGGACT-3′) and GAPDH (F: 5′-CAGCCAGGAGAAATCAAACAG-3′, R: 5′-GACTGAGTACCTGAACCGGC-3′). All reactions were performed using the Applied Biosystems 7000 Sequence Detection System (Applied Biosystems, Foster City, CA, USA). Relative expression levels were calculated as ratios normalized against those of GAPDH. Comparative quantification was determined using the 2−Δ ΔCt method.
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10

Quantifying Hippocampal Gene Expression

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Total RNA of the hippocampus was isolated using a Eastep® Super RNA extraction kit (Promega, Shanghai, China) followed by reverse transcription with a GoScript™ Reverse Transcription Kit (Promega, Shanghai, China) according to the manufacturer’s protocol. Finally, RT-PCR was performed with GoTaq® qPCR Master Mix (Promega, Shanghai, China) and specific primers (Sangon Biotech, Shanghai, China). The relative fold change in gene expression was calculated with the 2−ΔΔCt method with GAPDH as the internal control [34 (link)]. The primers used to detect TNF, IL-6, IL-1β, KCC2, and GAPDH mRNA were as follows:

TNF forward: 5’-CTGTGAAGGGAATGGGTGTT-3’;

TNF reverse: 5’-CAGGGAAGAATCTGGAAAGGTC-3’;

IL-6 forward: 5’-GGCCCTTGCTTTCTCTTCG-3’;

IL-6 reverse: 5’-ATAATAAAGTTTTGATTATGT-3’;

IL-1β forward: 5’-AGTTGACGGACCCAAAAG-3’;

IL-1β reverse: 5’-AGCTGGATGCTCTCATCAGG-3’;

KCC2 forward: 5’- AGGTGGAAGTCGTGGAGATG-3’;

KCC2 reverse: 5’-CGAGTGTTGGCTGGATTCTT-3’;

GAPDH forward: 5’-GACATGCCGCCTGGAGAAAC-3’;

GAPDH reverse: 5’-AGCCCAGGATGCCCTTTAGT-3’.

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