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All of the tested genes were selected based on the microarray analyses (see below).
Expression ratios for individual genes were examined by microarray analyses (see Supporting Information, Table S1).
The relative expression level of each gene was highly correlated with the data obtained by microarray analyses (see Supplementary Fig. 2).
RT-PCR analysis performed on RNA isolated from untreated and T4-treated parasites confirmed the results of the microarray analyses (See Additional File 1).
For the top 50 up- and downregulations of all performed microarray analyses, see Additional file 4. For brevity, only one Gene Ontology (GO -term is GO -termr each gene (obtaised with bioDBnet [ 97]).
Although most of our best scoring promoters do not correspond with the genes identified in our microarray analyses (see below), these data seem to be meaningful because the predicted candidates belong to the same functional categories of those up-regulated in citrus epicotyls in response to PthA/PthC expression or in Xc-infiltrated leaves in the presence of Ch (Additional files 1, 2, 3).
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For detailed DNA microarray data description and analyses see [ 11].
We tested both groups at the same time to allow for paired microarray and Cyber-T analyses (see below).
The results of the analysis reported by Brunskill et al. (Brunskill et al., 2008) can be accessed on the GUDMAP website (http://www.gudmap.org/gudmap/pages/genelist_folder.html) and researchers can also download raw microarray data for their own analyses (see http://www.gudmap.org/Help/Download_Help.html).
In the present study, we reanalyzed the microarray data for genes identified from bioinformatics analyses (see above) as mapping adjacent to the TgPWS/TgAS deletion.
For further details of procedures and analyses, see Additional file 7. Microarray gene expression data from this study have been deposited in the Gene Expression Omnibus as submission GSE43994.
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