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MAF representation of biological samples links individuals, samples, RNA extracts and labelled extracts, each with a many-to-many cardinality.
Labelled extracts were hybridised to whole-genome bead array (HumanWG-6 v3.0 Expression BeadChip) on an Illumina BeadArray reader.
It also includes the concentration values of the reference probes (SP) and the concentrations of labelled extracts of samples and the Standard Probes with the Frequency of Incorporation (FOI) of the dyes in these samples.
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Defined amounts of 13C-labeled cells were quenched and extracted together with defined amounts of natural labeled extracts.
Free non-incorporated Cy3 and Cy5 dyes, were separated by applying the labeled extracts on SigmaSpin post-reaction clean-up columns.
In addition to the labeled extracts, natural-abundance (unlabeled) extracts were generated as controls.
Evaluation of the filtering effectiveness was accomplished by comparing the number of credentialed features found in unlabeled and labeled extracts.
Fully labeled extracts have also been applied to the differentiation of biogenic and exogenous features in LC MS data.
Metabolites in the unlabeled cultures were quantified using established methods, 1) and these levels were used as a benchmark for the labeled extracts.
To quantify metabolites in the labeled extracts, a second set of unlabeled cultures was grown from the same starter in a medium containing unlabeled glucose.
Mashego et al. developed "mass isotopomer ratio analysis of U-C labeled extracts" (MIRACLE) in which U-C labeled metabolites obtained from yeast grown in defined culture medium are mixed with unlabeled sample extracts to improve quantitation.
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