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Specific primers

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Specific primers are short, synthetic DNA sequences designed to target and amplify specific regions within a DNA sample. They act as anchors for the DNA polymerase enzyme, initiating the DNA replication process during techniques such as Polymerase Chain Reaction (PCR). Specific primers enable the selective amplification of target DNA sequences, facilitating various applications in molecular biology and genetics.

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47 protocols using specific primers

1

Quantitative PCR Protocols for Gene Expression

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Total RNA was purified from cells using RNeasy Mini Kit (20–74104, Qiagen) and reverse transcribed using High-Capacity cDNA Reverse Transcription Kit (4368814, Thermo Fisher Scientific) with RNasin Plus RNase Inhibitor (N2615, Promega). The cDNA from each sample was applied in 20 μl reaction mix using Power SYBR Green PCR Master Mix (AB-4367659, Thermo Fisher Scientific) with specific primers (Sigma-Aldrich). Primer sequences were as follows: human MANF, 5’-GGG CGA CTG CGA AGT TTG TAT-3’, 5’- GTG CTC AGG TCG ATC TGC TT-3’; human PD-L1, 5’- TAT GGT GGT GCC GAC TAC AA-3’, 5’-TGG CTC CCA GAA TTA CCA AG-3’; human SERCA, 5’- CAT GAC AAC CCA CTG AGA AGA GAA-3’, 5’- CGA AGG TCA GAT TGG TCT CATATTT-3’; human GAPDH,5’-TGCACCACCAACTGCTTAGC-3’, 5’-GGCATGGACTGTGGTCATGAG-3’; Murine MANF, 5’- CCACCATATCCCTGTGGAAA-3’, 5’- CGTCCAGGATCTTCTTAGC-3’; Murine PD-L1, 5’-GCA TTA TAT TCA CAG CCT GC-3’, 5’-CCC TTC AAA AGC TGG TCC TT-3’; Murine GAPDH, 5’-TAT GTC GTG GAG TCT ACT GGT-3’, 5’-GAG TTG TCA TAT TTC TCG T-3’.
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2

Hippocampal Gene Expression Analysis

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Total RNA from hemi-hippocampi homogenates was extracted by using the NZY total RNA isolation kit (NZYTech, Lisboa, Portugal) following the company’s datasheet. The total RNA was measured by Nanodrop 1 000 spectrophotometer (Thermo Fisher Scientific, MD, USA), so, 1 µg of RNA was reverse transcribed to obtain cDNA by using oligo(dT) and random primers of the first-strand cDNA synthesis kit (NZYTech, Lisboa, Portugal). All PCRs were performed using supreme NZYTaq DNA polymerase (NZYTech, Lisboa, Portugal) with specific primers (Sigma-Aldrich, Milan, Italy) for tumor necrosis factor-α (TNF-α, forward primer 5′-CAGCCGATGGGTTGTACCTT-3′ and reverse primer 5′-CCGGACTCCGCAAAGTCTAA-3′), interleukin-1β (IL-1β, forward primer 5′-GGACCCCAAAAGATGAAGGGC-3′ and reverse primer 5′-GGAAAAGAAGGTGCTCATGTCC-3′), and IL-10 (forward primer 5′-GCCCTTTGCTATGGTGTCCT-3′ and reverse primer 5′-CTCTGAGCTGCTGCAGGAAT-3′). Glyceraldehyde 3-phosphate dehydrogenase (GAPDH, forward primer 5′-GCTACACTGAGGACCAGGTTGTC-3′ and reverse primer 5′-CCATGTAGGCCATGAGGTCCAC-3′) was used as reference gene.
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3

Quantification of apoptosis-related genes

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Total RNA of Jurkat cells were isolated with the EZ-RNA II total RNA isolation kit (BI, Biological Industries, Israel) according to manufacturer’s instructions at 24 h after plasma exposure. Quantification of RNA was carried out using a Nanodrop 2000 (Thermofisher Scientific). cDNA was synthesised by reverse transcriptase reaction using SensiFAST cDNA Synthesis Kit (Bioline, UK). Polymerase chain reactions were carried out using SYBR Green Master Mix (ThermoFisher Scientific) and specific primers (Sigma-Aldrich) for P53 (NM_001126114.1), BAD (NM_004322.3), BID (NM_197966.2) and GAPDH (NM_002046.3). The expressions of GAPDH were used as endogenous controls for normalisation. The changes in mRNA expression of P53, BAD and BID were analysed using the threshold cycle 2 -ΔΔCt method.
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4

Azoxymethane-induced Colorectal Cancer Model

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Azoxymethane (AOM), 10 % (v/v) neutral buffered formalin, TRI Reagent®, and specific primers were bought from Sigma (St. Louis, MO, USA). Dulbecco’s Modified Eagle Medium (DMEM), RPMI-1640 medium, Mycoplex™ fetal bovine serum (FBS), penicillin and streptomycin (100×), and trypsin EDTA (1×) were obtained from PAA Laboratories GmBH (Pasching, Austria). Colorimetric assay kit for caspase was bought from Genscript Corporation Inc (Piscataway, NJ, USA). High capacity RNA-to-cDNA Kit and SYBR® Select Master Mix (CFX) were purchased from Applied Biosystems (Foster City, CA, USA). Western blotting reagents were purchased from Bio-Rad (Hercules, CA, USA). All other chemicals and reagents used were of analytical grade and bought from Sigma-Aldrich (St. Louis, MO, USA).
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5

RNA Isolation, cDNA Synthesis, and qPCR Analysis

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Total RNA isolation and cDNA synthesis were performed using mirVana miRNA isolation kit (Life Technologies) and Maxima First-Strand cDNA Synthesis Kit (Thermo Fisher Scientific) following the respective manufacturers’ protocols. SYBR green–based qPCR analyses were conducted using specific primers purchased from Sigma-Aldrich (St Louis, Mo) (see Additional file 1: Table S1). All samples were tested in triplicate by using the GoTaq-qPCR Master Mix kit (Promega, Madison, Wis), with thermal cycling parameters of 95 °C, 15 s; 60 °C, 60 s each cycle for 40 cycles, at a thermal changing rate of 1.6 °C/s using ViiA 7 PCR machine (Applied Biosystems, Carlsbad, CA). Mean cycle thresholds (Ct) values were analyzed, and the relative gene expression normalized to housekeeping gene PGK1 was calculated using the 2-ΔΔCt method.
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6

Quantitative PCR Analysis of Gene Expression

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Total RNA was extracted with the RNeasy mini kit (#74106, Qiagen) according to the manufacturer’s introduction. RNA quality was assessed using NanoDrop 2000 and a total of 400ng RNA were used for reversed transcription using High-Capacity cDNA Reverse Transcription Kit (#4375575, ABI) with random primers. Quantitative real-time PCR was performed by BIO-RAD CFX96 real time PCR system with SYBR Green Mix and specific primers (Sigma). Data were normalized to the expression of housekeeping GAPDH gene and the relative abundance of transcripts was calculated by the 2−ΔΔCt method.
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7

Metagenomic DNA Plasmid Construction

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The plasmids were prepared by amplifying the gene encoding the metagenomic DNA of the samples extracted for the sequences available in the LBMP55 . The following specific primers (Sigma-Aldrich) were synthesized using the commercial PCRBIO Ultra Mix 2 × Kit26 (link): forward 5'-TATAgaattcTTCGGACGCAATCCAGACACCAATCC-3', which contains the restriction site EcoRI, and reverse 3'-TATAaagcttTTACTTGAACAGCAATTGAG-5', which contains the restriction sites EcoRI and HindIII. The fragment corresponding to the gene was purified by the Zymoclean Gel DNA Recovery Kit from ZymoResearch. The vector pET28a ( +) (INVITROGEN) and insert were restricted with restriction enzymes (FastDigest EcoRI, Thermo Scientific; and FastDigest HindIII, Thermo Scientific) and dephosphorylated with the enzyme Fast Alkaline Phosphatase (1 U/µL, Thermo Scientific). The connection between the insert and the vector was performed according to the protocol of Sambrook and Russel56 (link) using the T4 DNA ligase enzyme (New England Biolabs) in a 3:1 ratio (insert: vector).
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8

Primer Design and Synthesis for Gene Analysis

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Specific primers were manually designed and synthesized by Sigma-Genosys. Information on primer sequences and accession numbers of gene nucleotide sequences is shown in S1 Table.
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9

Quantitative Analysis of Melanocyte Gene Expression

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The total RNA was extracted from melanocytes using TRIzol Reagent. Next, melanin polymers were removed from RNA extracts by the use OneStep™ PCR Inhibitor Removal Kit (Zymo Research, Irvine, CA, USA). The total amount of RNA was measured using a microvolume spectrophotometer DS-11 (DeNovix®, Wilmington, DE, USA). Quantitative RT-PCR analysis was performed using SensiFAST™ SYBR No-ROX kit (Meridian Bioscience, Cincinnati, OH, USA) and specific primers for MITF, TYR and GAPDH genes (Sigma-Aldrich Inc., Germany). The primer sequences were presented in Table 1. The measurement was made using LightCycler® 480II (Roche, Penzberg, Germany) according to the following reaction parameters: 45 °C for 10 min, 95 °C for 2 min, 45 cycles of 95 °C for 5 s, 60 °C for 10 s, 72 °C for 1 min and the final extension for 10 min at 72 °C. The mRNA levels were calculated using the 2−ΔΔCt method. The obtained results were normalized using GAPDH expression and converted into expression level relative to the control.
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10

RNA Extraction and Quantification Protocol

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Right ventricles were crushed in TRIzol for RNA extraction as previously described 25. Cell RNA extractions were performed using the TaKaRa CellAmp Direct RNA kit (Clontech Saint‐Germain‐en‐Laye, France) as per the manufacturer's protocol. For miR‐322‐5p measurements, RNA was reverse‐transcribed (RT) using miR‐322‐5p and U6 Applied Biosciences TaqMan primers suspended in 1x TE buffer as per the manufacturer's instructions. cDNA was used for qPCR with TaqMan fluorescent probes for miR‐322‐5p and U6 according to the manufacturer's instructions. mRNA was measured via Omniscript RT (Qiagen, Manchester, UK) with random primers (Promega, Madison, WI, USA) as per the manufacturer's protocol. cDNA was diluted 1/10 with deionised water and used in qPCRs with QuantiFast SYBR Green (Qiagen) and specific primers (Sigma, Poole, Dorset, UK) for targets of interest as previously described 26.
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