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By careful design of nucleotide dispensation order, multiple SNPs may be analyzed in 1 single sequencing reaction by using a unique primer for each desired SNP.
Each polymorphic site was amplified by PCR (PCR primer sequence of each SNP is available on request) in a 15-μl volume containing 3% dimethyl sulfoxide and 0.75 units of Taq DNA polymerase (Promega Co., Japan) using a unique primer set.
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Additionally, accurate amplification is achieved by reduction of nonspecific amplification using a unique asymmetrical primer set.
Individual libraries were prepared using a unique index primer in order to allow for pooling of multiple samples prior to sequencing.
We studied 4 B. anthracis specific rpoB SNPs located at positions 911, 912, 913, and 914 in duplex sequencing reactions by using a unique sequencing primer for each desired SNP in a collection of 17 anthracis and 10 non-anthracis Bacillus strains.
Cloned isolates were screened to verify homologous recombination (Fig. S4) using a unique 5'-primer upstream of each genomic fragment used to tag the locus in combination with a common YFP primer or a unique 3'-UTR primer to confirm loss of the wild type locus (see Fig. S4 for screening design and results).
In brief, first strand cDNA was prepared using a unique first strand DNA/RNA chimeric primer mix and reverse transcriptase.
First strand cDNA is prepared from total RNA using a unique first strand DNA/RNA chimeric primer mix.
Total RNA was amplified using the NuGEN™ Ovation™ RNA Amplification System V2. First-strand synthesis of cDNA was performed using a unique first-strand DNA/RNA chimeric primer mix, resulting in cDNA/mRNA hybrid molecules.
Total RNA (50 ng) was amplified using the NuGEN™ Ovation™ Whole Blood Reagent and NuGEN™ Ovation™ RNA Amplification System V2. First-strand synthesis of cDNA was carried out using a unique first-strand DNA/RNA chimeric primer mix, resulting in cDNA/mRNA hybrid molecules.
To confirm P. ovale subtyping, a nested PCR amplification plus sequencing targeting cytochrome (Cyt) b was performed (3 ) in 3 samples of each group, by using a unique second amplification (nested) reaction with primers Cyt b 2F and Cyt b 2R.
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