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A reference design was used for microarray hybridizations, such that all RNA samples were labelled using Cy3 and co-hybridized with Cy5 labelled CRR pool.
A reference design was used for microarray hybridizations, such that all RNA samples were labelled using Cy3 and co-hybridized with Cy5 labelled common reference RNA CRRR) pool as described previously [ 24].
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Enrichment analysis performed by Gene Ontology (GO) Term finder tool showed enrichment for several biological categories among the genes up-regulated in the microarray hybridization such as transport and transmembrane transport and response to stress.
Future microarray based approaches may make it possible to dispense with the genotyping of individuals entirely, provided that a very large number of SNPs can be multiplexed in a single microarray hybridization such that it immediately provides a reliable map position.
In each case, replicate microarray hybridizations were carried out such that a p value could be calculated for each difference in gene expression.
Similar considerations regarding cDNA length and distance from the 3' prime end apply to other workflows that rely on cDNA synthesis, such as microarray hybridizations, in cases where oligo-dT priming is used.
The reduced yield as shown here is a result of aRNA degradation and this is a relevant point here to be made, because this might (and does) have an effect on post-amplification procedures such as microarray hybridizations.
RNA concentration and quality were determined with an RNA 6000 Pico LabChip® kit using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc .. Samples were paired for microarray hybridizations within sex and within litter such that extreme phenotype males and extreme phenotype females within a litter were paired on microarrays.
Therefore, comparative DNA microarray hybridizations are typically carried out in such a way that the relevant genes of the wild-type control are repressed and those of the mutant strain are de-repressed [ 39].
The relevance of this problem becomes apparent in experiments that use large datasets such as in DNA microarray hybridizations.
Microarray hybridizations were performed in triplicates for each strain.
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