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Based on the collection of the most comprehensive microarray data in ROAD (Table 2), we also developed co-expression analysis tools in ROAD.
Furthermore, 223 of the known miRNAs we identified and characterized in our sequencing datasets were not represented on even the most comprehensive microarray.
The Illumina Infinium HumanMethylation450k microarray is one of the most comprehensive microarray platforms available for the study of genome-wide DNA methylation in humans.
A more recent investigation into stilbene synthase expression during grape ripening with the latest and most comprehensive microarray platform showed low expression of STSs in all stages of berry development until post-harvest [ 67], suggesting that the precise timing of berry harvest could be a vital determinant in stilbene, and thus resveratrol, content in wine.
The Infinium HumanMethylation450 (HM450) Beadchip array (Illumina), the successor to the HM27, enables the detection of DNA methylation levels at 486,685 CpG dinucleotides across the genome and is one of the most comprehensive microarray methods to date for investigating the "methylome" [ 9].
The last version of Illumina's bead array, Infinium HumanMethylation450 (HM450) Beadchip, is cost-effective, requires DNA amounts as low as 300 ng, enables the detection and quantitation of DNA methylation levels at 486,685 CpG sites across the genome and represents one of the most comprehensive microarray methods to date for investigating the methylome [ 12].
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Here we describe the Rice Oligonucleotide Array Database (ROAD,http://www.ricearray.org), which integrates the most comprehensive public microarray datasets and provides several functional analysis tools.
Berry transcriptional profiles were analyzed during ripening using the most comprehensive grapevine microarray available to date, representing 29,549 genes from the most recent 12X grapevine V1 gene prediction http://srs.ebi.ac.uk/.ac.uk/
GeoChip 3.0 is the most comprehensive DNA microarray currently available for studying microbial communities associated with biogeochemical cycling, global climate change, bioenergy, agriculture, land use, ecosystem management, environmental cleanup and restoration, bioreactor systems, and human health.
Finally, we evaluated the performances of a custom microarray derived from this catalog, and found that this microarray was more informative than one of the most comprehensive grape microarrays available to date, the GrapeArray 1.2 that we developed within the Italian-French Public Consortium for Grapevine Genome Characterization.
In fact, the microarray designed on the unigenes from the normalized library proved to be more informative than one of the most comprehensive grape microarrays available to date, the GrapeArray 1.2 developed by the Italian-French Public Consortium for Grapevine Genome Characterization.
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