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We attempted to re-analyze the microarray data published by Cantuti-Castelvetri et al. [11] according to our criteria.
Of the 219 papers using microarray data published from January 1 to July 1 , 2010 less than ten percent addressed this issue (NCBI GEO database, studies with more than 30 samples)[9].
The diagram shown in Figure 7 integrates our transcriptome and proteome datasets of the response to carbon starvation, with regulatory pathways derived from microarray data published for CtrA [31], FixK [27], and LexA [52] (See Tables 2 and S8).
Consistent with this, Slfn4 was induced in macrophages in response to adenovirus infection (AI, unpublished data), and microarray data published by others reported up-regulation of Slfn4 mRNA in BMM upon infection with Sendai virus [33] and in the lungs of influenza A/PR/8/34 virus infected mice [34].
Furthermore we compared the results obtained with RNA-seq with microarray data published in a previous study [ 18].
We use the publicly cDNA and ratio-transformed oligonucleotide microarray data published by Spellman et al. [ 2, 29].
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To test whether native gene expression of our target genes correlates with the embryonic lethality phenotypes, we downloaded microarray transcriptome data published by Grishkevich et al. (2012).
In silico expression profiling (heatmapping) was performed using the Bio-Array for Plant Biology (BAR) eFP (electronic fluorescent pictograph) browser, which is based on re-normalized Affymetrix® microarray expression data published previously [ 81, 82].
In this study, we utilize the microarray cell cycle data published by Spellman et al., which contains expression profiles of 6178 yeast genes during the cell cycle [ 2].
However, changes in expression of these genes were either verified by qPCR and direct spot visualization in BASE or were present in our comparative analysis of our microarray data with data published by van der Graaff et al. [ 22].
In contrast, our metaanalysis of exon microarray data with published data sets revealed that RMS samples had an expression profile more similar to neuronal cells and patients than mesenchymal stem cells.
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