Interestingly, while these three genes display discordance among the microarray platforms, all four quantitative platforms show comparable results.
In this study, we developed an oligo microarray platform using all available I. multifiliis expressed sequence tag (EST) information as well as probes designed through comparative genomics to other protozoa.
The Breakthrough 17K microarray platform and all primary microarray data have been submitted to Array Express (ArrayExpress submission number E-TABM-180).
Samples from 10 patients were tested on the 385k NimbleGen oligonucleotide microarray platform, and all of the previously identified and validated copy-number variations were detected by the automated HMM algorithm.
Our study is the first to use a whole-genome DNA microarray platform covering all known and predicted genes to assess the effect of cell-incorporated radionuclide (I) on transcriptional response in primary human cells.
In general, RT-qPCR results confirmed the regulation trend seen in the microarray platform for all the 11 genes analyzed with very similar values using either GAPDH or ACTB for normalization.
The oligonucleotide microarray platform represented all confirmed and putative bovine mRNA features available (31 481) and provided an increase in gene number relative to the BoMP array utilized by Jensen et al. (2008).
Of these genes, 1,701 are represented on the Affymetrix HG-U95A2 microarray platform, common to all data sets considered in the present study (Table S1) Although the array covers only about 40% of the whole Membranome (Fig. 1A), the internal representation of all major functional classes – as defined by Panther [22] - is strictly maintained (Fisher exact test p-value<0.001 p-value<0.001
Second, to minimize the affects of data variability arising from technical issues, we chose a single microarray platform on which all downloaded experiments were performed.
Today, a large portion of microarray platform providers make all probe sequence information available; in addition, MIAME guidelines require submission of probe sequences for each spot on a microarray [ http://www. mged.org/Workgroups/MIAME/miame.html].
