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Divergence was reported in a microarray study measuring gene expression across five sets of environmental perturbation (heat shock, oxidative stress, nitrogen starvation, DNA damage, and carbon source switching) between S. cerevisiae, S. paradoxus, S. mikatae, and S. kudriazevii.
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We first compared our proteomic dataset to data from previous microarray studies measuring transcriptional changes due to rapamycin treatment in yeast [6], [7].
Moreover, this pattern is consistent across independent microarray studies measuring response to different artemisinin derivatives (Fig. 1a).
We can integrate different experiments that measure the same biological entity, such as microarray studies measuring tumor versus normal gene expression differences on different experimental platforms.
To assess Keratin 18 expression in a panel of cell lines, we used the same samples as in Figure 4F (i.e. independent samples from 3 IPF and 3 control fibroblast lines which were part of the microarray study) and measured protein abundance by immunoblot (mammary epithelial cells served as a positive control, Figure 6B).
To assess whether relationships existed between expression pattern and the P. infestans core motifs, we used data from a microarray study that measured mRNA at five sequential life stages [ 47].
While microarray studies assess gene expression levels by measuring hybridization intensities to the relevant probes [1], SAGE studies use portions of cDNA transcripts known as SAGE tags that are concatenated, cloned, and sequenced to provide a quantitative measure of the transcripts levels in the cell [2].
The microarray data we used in this study measures mRNA levels in yeast cells in response to environmental changes [ 10].
A second study measured gene expression in a set of four knockout human cell lines across ten laboratories using three different microarray platforms [ 18].
The results of the microarray study were confirmed by measuring the expression of 4 differentially regulated genes (Table 2) using Real-Time quantitative PCR (RT-qPCR).
DNA microarrays have been used to measure changes in host cell gene transcription during infection, with an aim to infer the mechanisms and strategies applied by Ap [ 19- 24], but no microarray studies that directly measure Ap transcription have been published.
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