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For the microarray experiment, we prepared 18 RNA samples (3 conditions (control, SiAF, and SiNF) × 2 time points (1 and 7 days after the beginning of fog treatment) × 3 biological replicates).
In a two-color microarray experiment, we consider the issues of determination of which mRNA samples are to be labeled with which fluorescent dye and which mRNA samples are to be hybridized together on the same slide.
For the microarray experiment, we used total RNA prepared from shoots, roots, panicles, and callus.
To confirm the changes in gene expression observed in the microarray experiment, we performed quantitative real time PCR (qRT-PCR) for a select number of genes.
In order to confirm the gene expression changes obtained in the microarray experiment, we performed real time-PCRs using SYBR Green I Dye chemistry.
Applying Analysis of Functional Annotation (AFA) on the data set from the above microarray experiment we found that several genes of the HR repair and DNA damage response pathway are downregulated upon HDAC inhibition.
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Using 3,934 diverse mouse microarray experiments we found striking similarities in transcriptional system regulation between human and mouse.
To validate our microarray experiments, we carried out real time PCR analysis of some of the identified genes.
At each of the time-points at which RNA was obtained for microarray experiments, we quantified the expression of at least one transcript.
Beside the scores of the candidates and the fold-change derived from the microarray experiments, we also present known links to similar diseases with related phenotypes.
To confirm gene expression patterns derived from our microarray experiments, we performed real-time RT-PCR with four selected genes that were down-regulated in the ΔpdeH mutant.
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