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Primer premier 7

Manufactured by Premier Biosoft
Sourced in United States

Primer Premier 7.0 is a software tool for primer design. It facilitates the selection of optimal primer sequences for use in polymerase chain reaction (PCR) and other DNA amplification techniques.

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3 protocols using primer premier 7

1

Quantitative Real-Time PCR Validation

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Quantitative real-time polymerase chain reaction (qRT-PCR) was performed using a FastStart Universal SYBR Green Master kit (Roche Diagnostics, Shanghai, China). qRT-PCR primers (Table 1) were designed from published target sequences and previously reported (Adams et al., 2009 (link)) with Primer Premier 7.0 software (Premier Biosoft, Palo Alto, CA, United States). qRT-PCR was performed on a LightCycler480 (Roche Applied Science, Mannheim, Germany), the products of which were purified by using a DNA gel extraction kit (Takara Bio Inc., Tokyo, Japan). For the purposes of assay validation, purified products were cloned into pMD19-T and sequenced to verify correct target amplification.
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2

Sperm RNA Extraction and RT-PCR Analysis

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Each sperm pellet was homogenized in 500 μL of TRIzol reagent at room temperature for 30 minutes. Then 200 μL of chloroform was added and shaken for 15 seconds, following centrifugation at 12,000 × g for 15 minutes at 4 °C. The upper supernatant was collected and precipitated using 500 μL isopropanol. After centrifugation of 12,000 × g, pellet was washed by 70% ethyl alcohol and resolved in sterile diethypyrocarbonate (DEPC) water. Complementary DNAs (cDNAs) were synthesized according to the instructions provided using avian myeloblastosis virus reverse transcriptase (Promega, Madison, WI). Primers were designed using Primer Premier 7.0 software (PREMIER Biosoft International, Palo Alto, CA) and each primer was submitted into an National Center for Biotechnology Information (NCBI) BLAST search to ensure specificity for the target mRNA. Real-time RT-PCR was performed under conditions of 2 minutes at 95 °C, followed by 15 seconds at 95 °C and 50 seconds at 65 °C for 40 cycles. Data were analyzed using the GeneAmp5700 Sequence Detection System software (version 1.1; Applied Biosystems, Foster City, CA) and were converted into threshold cycle (CT) values. All samples were normalized according to b-actin content. The formula 2–△Ct was used to calculate the relative mRNA levels.[20 (link)]
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3

Microsatellite Mining and Primer Design

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Perl script MISA software (MISA http://pgrc.ipk-gatersleben.de/misa/; RRID:OMICS_00110) was used to mine microsatellites from the assembled sequences. Sequences with at least nine repetitions for dinucleotides, six repetitions for trinucleotides, and five repetitions for tetra-, penta-, and hexa-nucleotides, excluding the polyA and polyT repeat, were identified. Dinucleotide repeats such as AT/TA and CT/GA were treated as the same type of repeat motif.
Primer Premier 7.0 software (PREMIER Biosoft International, Palo Alto, CA) was used to design appropriate primers from the flanking sequences, based on the following criteria: primer length of 18–22 bp (optimally 20 bp), GC content of 40–60%, annealing temperature (Tm) of 50–60°C (with the Tm of forward and reverse primers differing by no more than 4°C), and expected amplified product size of 100–400 bp. Primers were synthesized by Invitrogen Biological Engineering Technology & Services Co., Ltd (Shanghai, China).
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