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5 protocols using forward and reverse primers

1

Quantitative Analysis of ACE-2 Gene Expression

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RNAs were extracted using RNeasy Mini Kit (Qiagen) and were frozen at −80°C. We used Nano‐Drop 2000c (Thermo) to evaluate the quality and quantity of isolated total RNAs. In this regard, RNA samples with A260/A280 ratios of >1.8 were selected for quantitative analysis. First‐strand complementary DNA (cDNA) synthesis was initially performed using the Revert Aid First Strand cDNA Synthesis Kit (Thermo Scientific, Fermentas). Then, real‐time quantification was performed using Rotor gene‐Q real‐time PCR system (Qiagen). Each real‐time PCR (10 μL) included 1 μL of reverse and forward primers (Exiqon), 5 μL of Ampliqon real Q plus 2× master mix green (Ampliqon), and 4 μL of diluted cDNA. Primer sequences for the ACE‐2 gene were F: 5′‐TCCATTGGTCTTCTGTCACCCG‐3′, R: 5′‐AGACCATCCACCTCCACTTCTC‐3′. The reactions were incubated in a 72‐well optical strip at 95°C for 15 min (enzyme activation), followed by 95°C for 20 s and 60°C for 60 s (40 cycles). All reactions were run in triplicate. After the reactions, the mean Ct was determined from the triplicate PCRs. We used Ct values to evaluate the expression levels of the ACE‐2 gene. It should be noted that Beta‐actin was the endogenous control gene to normalize RNA contents among different samples. The expression value of the ACE‐2 gene relative to internal controls was determined using the 2−ΔCt method.
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2

Quantifying Sperm miRNA Expression

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After liqufication, we centrifuged the semen samples for 10 min at 500 g. Then 1 ml FSB (Merck, Germany) was added to sperms pellet and somatic cells removed.TRIZOL reagent was used for isolation of the total RNA from the sperms based on kit protocols (Invitrogen Life Technology Co., USA). hsa-miR-449-a (MI0001648), hsa-miR-449-b (MI0003673), and hsa-449-c (MI0003823) were studied in this research. hsa-miR30a-5p (MIMAT0000087) and hsa-miR100-5p (MIMAT 0000102) were used as internal controls. Rotor gene-Q real-time PCR system (Qiagene, Germany) was used to quantifing of the RNA expression. Total amount of master mix was 10 µl and included 1 µl of reverse and forward primers (Exiqon, Denmark), 5 µl of Ampliqon real Q plus 2 × master mix green (Ampliqone, Denmark), and 4 µl of diluted cDNA. For enzyme activation we incubated master mix for 15 min at 95°C. Then reaction was runned in 40 cycle for 20 sec at 95°C and 60 sec at 60°C. Ct values was used for evaluation of expression rate of studied miRNAs. hsa-miR30a-5p and hsa-miR100-5p were used as the endogenous controls. The 2 - Ct method used for expression rate detection of target genes in comparision to internal controls.
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3

Isolation and Sequencing of Streptomyces sp. 16S rRNA

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For total DNA isolation, strains were cultivated in TSB medium for 3 days at 28 °C and shaken at 180 rpm. Total DNA was isolated by the salting-out procedure, as described in [13 ]. Amplification of the 16S rRNA gene was carried out using the primers 8F (5′-AGAGTTTGATYMTGGCTCAG-3′) and 1510R (5′-TACGGYTACCTTGTTACGACTT-3′). A polymerase chain reaction (PCR) was carried out in a total volume of 50 μL containing 2.0 μL of genomic DNA (~50 ng), 0.5 μL of each primer (100 pmol), 1.0 μL of deoxynucleotide triphosphates (10.0 mM each), 5.0 μL of 10 × PCR buffer, 0.5 μL of DNA polymerase (1 U/μL), 2.5 μL dimethyl sulfoxide and 38.0 μL of Milli-Q grade water. The PCR parameters were initial denaturation at 95 °C for 5 min, followed by 30 cycles of denaturation at 95 °C for 30 s, annealing for primers at 53 °C for 30 s and extension at 72 °C for 90 s. A final extension was carried out at 72 °C for 10 min. The received PCR products were visualized in 1% agarose gel and then purified using the QIAquick Gel Extraction Kit (Qiagen, Venlo, Netherlands) and sequenced with forward and reverse primers by Explogen LLC (Lviv, Ukraine). The 16S rRNA gene sequence of Streptomyces sp. Pv 4-95 was deposited in GenBank with the accession number OM763959.
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4

Quantitative RT-PCR Analysis of Chlamydia-Infected Mast Cells

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In each reverse transcriptase reaction, 150–300 ng of purified RNA was used to generate cDNA. Following genomic DNA elimination with gDNA wipe-out buffer (Qiagen, Germantown, MD, USA) at 42°C for 2 min, cDNA was prepared by setting up an RT-PCR reaction with RNA template, Quantiscript reverse transcriptase, Quantiscript RT buffer, and RT primer mix (Qiagen, Germantown, MD, USA) according to the manufacturer’s instructions.
Quantitative PCR (qPCR) reactions were set up with 1× SSo Advanced™ Universal SYBR® Green Supermix (Bio-Rad, Mississauga, ON, Canada), 250–500 nM of forward and reverse primers (Qiagen, Germantown, MD, USA or Bio-Rad, Mississauga, ON, Canada), and nuclease-free water in Bio-Rad CFX96 touch real-time PCR detection system. qPCR data were analyzed using CFX Maestro™ software. Gene expression values were determined using the formula ΔCq = Cq of the gene of interest − Mean of Cq of housekeeping genes, and normalized expression was then calculated as 2−(ΔCq). A predesigned 384-well PCR panel (Bio-Rad, acute inflammation response H384) was used to screen uninfected vs. C. trachomatis-infected mast cell gene responses according to the manufacturer’s instructions.
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5

Quantification of Gene Expression in Liver and Kidney

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Total RNA was isolated from the liver and kidney tissue using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.), and reverse transcribed into cDNA (1 µg) using a reverse transcription reagent kit (Promega Corporation, Madison, WI, USA). The PCR reactions were performed on the ABI 7,900 system (Applied Biosystems; Thermo Fisher Scientific, Inc.) in a 20 µl SYBR Green PCR reaction containing 1X SYBR Green PCR master mix (Applied Biosystems, Thermo Fisher Scientific, Inc.), 8 ng cDNA, and 10 nM forward and reverse primers (Qiagen GmbH), which were synthesized with the sequences listed in Table I. The reaction conditions were 95˚C for 10 min followed by 40 cycles of 95˚C for 15 sec, 60˚C for 1 min and 72˚C for 30 sec. Dissociation curves were generated to ensure that a single and specific product was amplified. Quantification cycle values (Cq) were analyzed using SDS2.4 software (Applied Biosystems; Thermo Fisher Scientific, Inc.).
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