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(A) Results obtained after statistical analysis with user-defined criteria to identify genes with very high expression in the desiccation stage of seed development in rice.
The remaining 25 genes with very low σ were discarded.
Primer efficiency tests revealed six of nine genes with very low expression levels (Ct>34).
This can happen for genes with very broad cytogenetically-derived gene mappings.
Strikingly, we found that methylation was even excluded from the first exon of genes with very low-level expression.
Notably, we used this stringent cut-off because we desired a smaller number of genes with very low false positive rates on which to focus our attention.
This scheme works well for most genes, but for genes with very large numbers of homologs, it takes a long time to compute all the pairwise alignments.
Therefore, genes with very low basal levels of expression (Table 2) show the highest fold change in response to Alk4*-Smad2/3 activation, suggesting that in ES cells the expression of these genes depends solely on P-Smad2/3.
However, this means that genes with very low expression in either PT or the SAGM-grown cells were probably excluded even though their difference in expression levels was far greater.
For some genes with very short exons, such as petB and petD, manual annotation was performed.
Clustering experiments showed that trends could be detected from genes with very low expression.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com