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View additional product information for GeneChip™ Human Gene 1.0 ST Array - FAQs (901087, 901086, 901085)
11 product FAQs found
Based on mitomap, approximately 87 exons from the mitochondrial transcriptome are represented on this array.
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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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-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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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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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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All annotation sources were considered. In cases where both strong support (i.e., aligned RefSeq mRNA sequences) and poor support (i.e., GENSCAN predictions) exist, both were used. Thus, a gene locus that contains a RefSeq mRNA will frequently contain probe sets representing not only the RefSeq exons, but also a number of other exons supported by other annotation sources. Slightly over half of the array is supported only by a single source and many of these are EST- or GENACAN- based annotations. See the GeneChip Exon Array Design Technical Note (https://tools.thermofisher.com/content/sfs/brochures/exon_array_design_technote.pdf) for a more comprehensive discussion of the content on the array.
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The majority of the splicing changes occur because of alternative exon usage or exon skipping, which will be captured with this type of array design. Fine modifications such as alternative 5' or 3' splice site usage with shifts of less than 25 bases will not be captured by this design.
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In many cases the Genechip probes do overlap quite heavily. Multiple probes, although overlapping, are utilized as they still provide separate physical measures of expression and add to the robustness of the platform. Care was taken to ensure that probes from the same probe set, however similar in sequence composition, are spatially separated on the array. In addition, the annotation library file contains information regarding how many independent probes there are, as well as the number of nonoverlapping probes, in each probe set. Independent probes are defined as those that have less or equal to 13 base overlaps with other probes in the probe set. This information provides additional insight and may be helpful to users when interpreting unexpected results.
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About 90% of the exon-based probe sets contain 4 probes for each PSR. The remaining 10% are roughly equally split between 3, 2, and 1 probes for each probe set.
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PSR is the smallest unit on the exon array for expression profiling and each PSR is represented by an individual probe set. In some cases, each PSR is also an exon; in other cases, due to variation in overlapping exon structures, the PSR can be a subset of the true biological exon. As a result, alternatively spliced exons from the same gene may overlap (i.e., alternative donor or acceptor site); however, PSRs have the property that they do not overlap each other in the genome space, except if annotations change with a newer version of the genome assemblies. In cases where multiple annotations infer different exon structures, that one exon cluster (a group of overlapping exons) will be divided into multiple PSRs. Therefore, in the final design, there are approximately 1,000,000 exon clusters represented by approximately 1,400,000 PSRs.
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Median is 123 bases, and minimum is 25 bases.
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