Are mitochondrial RNAs represented on this GeneChip Human Exon Array?
Based on mitomap, approximately 87 exons from the mitochondrial transcriptome are represented on this array.
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Can I use this GeneChip Human Exon Array to detect the expression of microRNAs?
Approximately 190 unprocessed human microRNA sequences from the Sanger MicroRNA Registry are represented on this array. Although the probe sets are present, the current WT Sense Target Labeling Assay has not been tested or optimized to efficiently label the very small RNA molecules. Therefore, the utility of the system to measure microRNA expression is uncertain at this moment.
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What kinds of annotation will be available for GeneChip Exon arrays?
-Information about the annotation types supporting each probe set
-Genome coordinates for all PSRs, probe sets, and probes
-Various quality information about the probe and probe sets (i.e., number of overlapping probes in a probe set)
-Some biological annotation (i.e., gene names)
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Which controls are included in the new GeneChip Exon array?
A variety of controls are included on the Exon Array, designed specifically to facilitate the application of genome-wide exon-level expression profiling. These controls include:
Intron controls--for approximately 100 genes with relatively constitutive expression, both exon-based and intron-based probe sets were tiled. The intron/exon normalization control probe sets can be used to monitor contamination from genomic DNA, hnRNA, as well as to provide a baseline for experiment quality control.
Hybridization controls--bioB, vbioC, bioD and cre
Poly-A RNA controls--lys, dap, phe, and thr
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If all sources are taken into consideration for the array design, will that result in over-fragmentation of the PSRs?
A significant amount of research was dedicated to developing optimal algorithms for generating the design to both ensure comprehensive coverage of putative exons and also prevent over-fragmentation. Many of these design criteria are discussed in the Genechip Exon Array Design Technical Note (https://tools.thermofisher.com/content/sfs/brochures/exon_array_design_technote.pdf), such as restricting exon fragmentation to only those ESTs with consensus splice sites.
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