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The sensitivity of the microarray was determined using DNA from 21 CMS patients possessing mutations previously characterized by capillary sequencing.
The number and identity of genes commonly affected in two platforms (e.g. SAGE study vs. DNA microarray) was determined.
RNA quality for samples later used in the microarray was determined using a Agilent 2100 Bioanalyzer (RNA 6000 NanoLabChip, Agilent, Waldborn, Germany).
To assess whether other junction genes, especially the members of the gap junction family, were also affected from the KO of Cx43, the gene expression of those junction genes available on the microarray was determined (supplementary material Table S4).
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The detection limits of the microarray were determined under these conditions by titration of chromosomal DNA and unlabelled amplicons followed by hybridisation to determine the levels of sensitivity that could be obtained with the microarray.
In addition, both the specificity and reproducibility of the microarray were determined using DNA from 5 healthy individuals.
Over-represented gene ontology categories for proteins changed by smoking and for proteins that were not detectably expressed by microarray were determined by comparing the corresponding RefSeq identifications numbers for these proteins against the complete set of 859 proteins detected by mass spectrometry in this set of experiments.
The correlation co-efficients between the set of signal ratios from each microarray were determined in a pair-wise manner.
Overall, mRNA expression levels of 17,816 RefSeq transcripts and full-length mRNA transcripts using the core probes of the exon microarray were determined, and the number of unique genes detected above background (DABG) was 11,112.
Optimal elongation conditions on microarray were determined in order to allow elongation reactions to go to completion. Figure 3 shows that there is a linear correlation between the defined methylation density of the standard clone dilutions and the (Cy5sam*Cy3pos)/(Cy5pos*Cy3sam) signal ratios.
The relationship between results obtained with qPCR-array and microarrays was determined.
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