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Two positive controls were designed for each SNP, to include allele-specific target sequence (without the addition mismatch) and the common primer (forward or reverse as appropriate), to test the ability of the assay to identify the SNP (Table 9).
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The BRAF V600E/wildtype duplex TaqMan assay used common primers (forward) 5′-CTACTGTTTTCCTTTACTTACTACACCTCAGA-3′, (reverse) 5′-ATCCAGACAACTGTTCAAACTGATG-3′, and specific probes (BRAF V600E) 6FAM-TAGCTACAGAGAAATC-MGBNFQ and (wildtype) VIC-CTAGCTACAGTGAAATC-MGBNFQ.
For each INDEL marker, one common primer (CP and twoo forward primers were designed: one inside (IN) and one outside (OUT) the deletion (Table 3).
In the next step, quantitative RT-PCR was performed in presence of Express Syber GreenER (Invitrogen) using the following primers: common forward primer 5′-aataaatcataaggccgtcatggtggcgaataa-3′ in combination with either L reverse primer 5′-aataaatcataatcgaaaacgacttccatgtct-3′ or 1D reverse primer 5′- aataaatcataacctcttctccccctttgtgt-3′ to detect L or 1D region respectively.
Where CP = Common Primer; inv = Inversion; F = Forward; R = reverse These MAMA were used to analyze several isolates within the Vollum branch.
Nineteen specific forward primers and a common primer annealing in the β-chain constant (Cβ) region were designed to amplify all Aotus Vβ families reported to date [11].
Multiplex PCR using genomic DNA as template was performed with a combination of three primers: a common forward primer located upstream of Hoppel insertion (Indy-hoppel±1S: 5'-CTACATTGTATACGGAGACATTCG G-3'); two reverse primers, one inside Hoppel (Indyhoppel+3A: 5'-CCATGTAAATTCGTTTCTTCGATC-3') and the other downstream of Hoppel (Indy-hoppel−1A: 5'-CATCTTTCGTCTTGCTATCAGCA-3').
This allows designing common primers for PCR, for examples, the forward and reverse primers for all font images now commonly contain gTCTTg and gTCTT, respectively.
Primers: F, forward primer; R, reverse primer Primers: F, forward primer; R, reverse primer.
Genotyping of Bcl-G-deficient mice was performed using a three-primer PCR reaction using a common forward primer (5′-TCCGTCCCATTATAACCCTA-3′), together with two reverse primers (5′-CTGGAACGACAGAGGGCAAA-3′ and 5′-TTACCATCACAGAGCCAGAA-3′).
SNP rs761142 was genotyped using allele specific PCR (common forward primer: CAACAGTTGGTTCTAGCAAAAGGA; reverse primer for reference allele: CCACACTGCTGGCTCTCTTGTAA; reverse for variant allele: CCACACTGCTGGCTCTCTTGTAC) as described [ 47].
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com