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Sequences were assayed using Sequencher (version 4.5; Gene Codes).
Within motif group I, two different sequences were assayed.
Different peptide sequences were assayed to determine how the sequence affects the rate of product formation.
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The enrichment of specific sequences was assayed using flow cytometry as explained below.
As with any genotyping assay, one must have knowledge of the sequences being assayed, therefore a practical limitation of the approach is the requirement for a priori knowledge of the TCR usage of the T-cell response under analysis.
Alternatively these higher miscall rates could be due to paralogous genomic sequences being assayed, although generally this has not been a major problem with the GGGT even in complex plant genomes [ 27].
All coding non-synonymous variants and coding indels detected in Sanger sequencing were assayed with PCR-directed orthogonal sequencing validation.
From this motif group only one putative cis-regulatory sequence was assayed, namely CCAACTAA, from which only R2R3-MYB TFs (17 genes) were also identified (Table 3).
In contrast, Li/LdSIDER2A 81 Rz activity was reduced and LmSIDER2A 81 Rz increased when the 20 nt-long wild type upstream sequence was assayed (see Figure 3C for activity and 3D for quantification of the cleavage products of the constructs shown in Figure 3A).
The abundance of the mtDNA-encoded template [from nucleotide (nt) 6409 to nt 6636] in the COX1 gene sequence was assayed (primers: forward CAT CCC TTG ACA TCG TG, reverse CTG AGT AGC GTC GTG G) and normalized using a nuclear-encoded template for the 18S gene (primers: forward CGGACAGGATTGACAGA, reverse: CCAGTCAGTGTAGCGC) (65).
Some of the potential promoter sequences that were assayed failed to show any transcriptional activity.
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