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Since Tetracystis intermedia (TEL170), T. pulchra (TEL173) and Tetracystis texensis (TEL175) from the Dunaliellinia clade did not show a clear TRAP pattern using the primer combinations mentioned above, TRAP products were cloned from reactions utilizing the primer set CAMV × T3AG2-C (fig. 5 E ).
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The single-tube RT-LAMP assay utilized a primer set with coverage for all the reported DENV strains particularly those common in the region.
Two micrograms of total RNA was then reverse-transcribed, and quantified by RT-qPCR utilizing the following primer sets and probe Sense: 5'-TCTTCACGCAGAAAGCGTCTA-3', Anti-Sense 5'-CGGTTCCGCAGACCACTATG-3', Taq-man FAM labeled probe 5'-/56-FAM/TGAGTGTCG/ZEN/TGCAGCCTCCAGGA/3IABκFQ/-3' 5'-/56-FAM/TGAGTGTCG/ZEN/TGCAGCCTCCAGGA/3IABκFQ/-3' 5'-/56-FAM/TGAGTGTCG/ZEN/TGCAGCCTCCAGGA/3IABκFQ/-3' 5'-/56-FAM/TGAGTGTCG/ZEN/TGCAGCCTCCAGGA/3IABκFQ/-3'
The primer set showed amplification of 480 bp product.
To further investigate the BSS results, we performed a second BS PCR on DNAs from subjects 75204 and 75205 utilizing a BS PCR primer set (primers BSS1438F and BSS3702R) that amplifies the distal D4Z4 region from both 4qA and 10qA for nested PCR.
This observation can be ascribed to the different specificity of the primer sets utilized in qPCR quantification, since the primers for Enterobacteriaceae recognize a broader spectrum of species than the ones for E. coli (Table 1).
ADB designed the primer sets.
The primer sets were designed using NCBI Primer-Blast.
K. Hamaguchi kindly provided the primer sets.
In cases where the conserved primer set failed, species-specific primer sets were implemented.
Analysis of the ROSA26 promoter utilized the primers ROSAF2: 5'-GGAAAYGTTATTGATYGTAYGGGGATT-3' and ROSAR3: 5'-ACTATCTCACAAAACRACTCCACCAC-3'.
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