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Thus, we conclude that the genome-wide microarray analyses described above identified an authentic set of CbfA-dependent genes and that we can use the ten genes being tested in real-time PCR measurements as representative of the microarray study and as a useful tool to investigate how individual CbfA domains are involved in this regulation (described below).
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Microarray experiments and analyses (described in detail under Methods), were carried out to identify significant gene expression level changes that were uniquely affected by GN-25 treatment in the context of the transformed SNAIL over-expressing cell line, Kras-HMLE-SNAIL, compared to GN-25 effects in the control Kras-HMLE cell line.
The DNA microarray analyses are described above.
Gene set testing and microarray analyses are described in the supplementary material.
We identified 45 genes whose expression was altered 2-fold or more by SSeCKS overexpression using at least three independent Affymetrix microarray analyses, as described in Materials and Methods, of RNA from S24 cells grown at 37°C in the presence or absence of tet.
These analyses are in agreement with oligonucleotide-based microarray analyses, and describe only a subset of significant genes with aberrant regulation in the exposed set.
The microarray analyses were performed as described previously (Hanada et al. [2013]) with the exception that two biological replicates were used.
DNA microarray analyses were performed as described previously [39], [40].
Microarray analyses were conducted as described previously [ 44].
Gene microarray analyses were performed as described before.
The selected samples were used for RNA extraction and microarray analyses, obtaining transcriptomic data, described in detail in a previous publication [ 17].
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