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The microarray design was deposited in the Gene Expression Omnibus (GEO) database and is available under accession number GPL5874 [ 8].
Although the microarray design was focused on clinical diagnostics, its application to further fields like quality control of food or water as well as veterinary medicine is imaginable.
Since the microarray design was based on a platform that permits flexible in situ oligonucleotide synthesis, a set of optimally performing probes could be defined by a selection approach that combined computational and experimental aspects.
Since we specifically intended to study desiccation- and rehydration-induced gene expression of the whole symbiotic lichen, which has been shown to tolerate desiccation better than either of its isolated partners [ 3], the microarray design was based on sequences prepared from whole lichen tissue.
The microarray design was based on the sequences including 66,418 ESTs (31,685 contigs and 34,733 singletons) from sweetpotato gene index established by Schafleitner et al. [ 27], 56,516 developed by Wang et al. and 58,681 generated in house [ 2, 51].
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The microarray design is available in BμG@Sbase (Accession No. A-BUGS-14; http://bugs.sgul.ac.uk/A-BUGS-14) and ArrayExpress (Accession No. A-BUGS-14).
CDSs that were not included in the microarray design were all transposase-encoding genes.
The microarray design is deposited in the ArrayExpress database (http://www.ebi.ac.uk/arrayexpress/) and the array is available to the International Aphid Genomics Consortium community.
The microarray design is, however, not fixed: a crucial advantage is that newly annotated genes can easily be added to this array.
The microarray designed was composed of 1,830 genes selected from the SUCAST Catalogue.
This suggests that all the microarray designs were comprehensive with respect to genome coverage, and that the fixed probe sets may not have been a main limitation in this study.
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