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Fig. 2 Microarray hybridization results from a blinded panel of 22 fecal samples and two positive reference materials including Norwalk (GI) and 186 (GII) strains.
Real time RT-PCR was used to validate the microarray hybridization results for seven of the genes detected as DE.
The real time PCR was performed on one linear round amplified cDNA according to the microarray protocol above to facilitate direct comparison with the microarray hybridization results.
Excluding clones that mapped to multiple Unigene clusters, we grouped the clones from each cluster into subclusters based on whether or not the microarray hybridization results derived from those clones yielded the same transcript length measurements.
Microarray hybridization results are available at GEO (http://www.ncbi.nlm.nih.gov/geo) under the accession number GSE42156.
*lower estimates of genomic content based on microarray hybridization results and validation methods.
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Overall, qRT-PCR analysis confirmed the variations in expression levels noticed in microarray hybridization assays resulting in an inflammatory signature in DCs treated with the highest dose of probiotic.
For these reasons, major commercial vendors now release the exact sequence of each of their probes, and reporting probe-level data from microarray hybridization and analysis results in publications and public repositories is preferred [ 2].
Furthermore, the expression levels of low abundance genes cannot be readily assessed by DNA microarray hybridization, since reliable results are usually obtained only for genes that are expressed in high or moderate levels.
Our microarray and in situ hybridization results showed that many photoreceptor genes appear to be co-regulated by Crx and Nrl, a finding which is corroborated by prior analyses of individual photoreceptor-specific CREs [26], [27].
Quantitative real-time PCR (qRT-PCR) was used to validate the microarray hybridization data, with the results confirming the microarray epxeriment's reliability (Additional file 1).
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