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Screened primer pairs giving good amplification were subsequently used to characterize genetic diversity among 23 accessions of tree peony (Additional file 2: Table S2).
In the pilot study, negative controls were run on all gels to check for contamination and replicate amplification was performed on 11 individuals from independent extractions for six of the screened primer combinations.
We initially screened primer sets for polymorphism using 58 individuals from three L. inflata populations: Petawawa, Ontario (n = 43); Martock, Nova Scotia (n = 8); and Petersham, Massachusetts (n = 7).
In this tool, candidate primers are firstly comprehensively identified using Primer3 software (Untergasser et al., 2012), and are subsequently screened under primer design criteria for LacZ assay as described (see previous section), and the screened primer pairs are further checked for off-target sites.
To determine suitability for RH panel typing, we screened primer pairs by PCR-amplification of DNA from river buffalo (the RH panel donor animal), A23 hamster (the RH panel recipient cell line), and cattle (positive control) fibroblast cells, followed by dissociation curve analysis of the products as described by Ririe et al. [ 29].
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We initially screened primers by amplifying fragments from our test samples and visualizing the product using gel electrophoresis.
In order to find the best set of primer tuples, we first have to create and screen primer tuples from the lists of valid primers for each restriction site to be studied.
Screening primers are denoted as black triangles, promoters are depicted as angled arrows and the t1t2t0-terminator is shown as a hairpin-structure.
Methods and Results: Fourteen microsatellite loci were characterized by screening primers developed using two simple sequence repeat (SSR)–enriched libraries.
For initial T. b. gambiense TAR clone screening ESAG6/7 screening primers ESAG7a (sense and anti-sense) were used (sequences in [ 34]).
For screening the rest of the T. b. gambiense TAR clones and all of the T. b. brucei and T. equiperdum TAR clones, screening primers ESAG6/7-311s and ESAG6-809as were used.
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