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Quantitative PCR was carried out by Taqman assay method using gene specific primers and probes from the Universal Probe Library (UPL), Human (Roche) as the internal oligonucleotide, according to manufacturer's instructions.
Xu et al. (2007) proposed a method using gene profiles generated from PubMed abstracts for gene disambiguation.
As an example, the authors demonstrated the new method using gene expression data for a cell line treated and untreated with heat shock.
Gene expression of matrix metalloproteinase (MMP) 2, MMP3, MMP13 and aggrecan (ACAN) gene was normalized with GAPDH and data evaluation was relative employing the ΔΔCT method using gene expression of unstimulated monocultures as calibrator.
For most applications, it is much faster than the conventional method using gene targeting in ES cells, which can involve many months of targeting vector construction, selection, and validation of targeted clones and achieving germline transmission from at least one clone.
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A fourth method used gene expression of ECs.
This method uses gene set enrichment, not individual gene expression, as the basis of its similarity.
The NJst method uses gene trees, which can include several individuals per species, and estimates a distance matrix between species.
The method uses gene expression profile Pearson correlation measures, magnitude of change, and signal-to-noise evaluations to categorize genes into patterns that represent co-expressed genes.
(Our method uses gene annotations for visualization and if provided will take advantage of them to slightly improve its sequence similarity calculations, but it does not require them to determine orthology).
Methods using gene information are based on differences in codon usage between highly expressed, lowly expressed and alien genes [ 45- 48].
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