511037 - FAQs

A candidate list of probe sets was obtained in collaboration with an external site based on a large number of tissue samples run on RG-U34 arrays. Criteria for selection included evidence of constitutive expression (detection in at least 95% of replicates) and minimal variation in signal across the tissues tested. The 11 probe pair probe sets for these transcripts were evaluated by hybridizing 11 tissues and 4 cell lines on Rat 230A and B arrays. One hundred probe sets were selected that had detection in at least 95% of replicates and had minimal signal variation. Preference was given to RefSeq sequences where possible, probe sets were selected to give a range of signal values and to represent 100 unique UniGene clusters.

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The normalization probe sets are the first 100 probe sets found after probe sets with an "AFFX" prefix. The *.msk file can be opened in Notepad or equivalent to view the list of probe sets. They are represented by probe sets 1415670 and 1415769.

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In order to provide an additional mechanism to normalize data, probe sets representing 100 constitutively expressed transcripts were tiled on both the Rat 230A and Rat 230B arrays. The normalization set was found to be expressed in a range of tissues and cell lines. The set was selected to represent a range of signal values from low to high. Furthermore, in-house experiments, there was minimal variation in signal for these probe sets in the tissue panel (%CV less than 40%).

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The Baylor College of Medicine Human Genome Sequencing Center (June 2002) assembly was used to design the Rat Set 230. Specifically, the genomic sequence was used for trimming low quality portions of EST sequencing reads and for improving orientation calls through the use for flanking intronic sequence. The probe sets themselves are constructed against the consensus sequence for cDNA sequence clusters. The Rat Set 230 is not a genome tiling product, but rather an mRNA expression product; thus the entire rat genomic sequence is not represented.

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Complete sequence information for the probes, target, and consensus/exemplar sequences represented on all catalog expression arrays, including the new Rat 230 Set, are available through the Support by Product page.

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The probes on the Rat 230 are designed to detect an anti-sense target prepared by the Affymetrix 3' biased assay, and these probes are annotated with the "_at" extension. The primary goal in probe selection is to select a probe set unique to single transcript or common among multiple transcripts from the same gene.

Often it is not possible to select a probe set that is unique to a single transcript because multiple transcript variants share common sequence. Such probe sets have the "_s" extension. Occasionally, it is not possible to select a unique or shared probe set. Such probe sets have the "_x" extension.

For more information, please review the "_s" and "_x" probe set descriptions.

Please note: There are no "_f", "_g", "_r", "_i", or "_n" probe sets in the Rat Expression Set 230 design opposed to the RG-U34 design. This is because the non-unique probe set types were simplified and adjusted to account for improvements to the probe selection rules.

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Briefly, during development, a tissue (11 tissues) and cell line (4 cell lines) panel was hybridized to both Rat 230 and RG-U34 arrays. This sample set was used to evaluate tissue-specific expression patterns and for studies to compare data from the previous and current designs, including analysis of variance. A set of 41 prelabeled spikes derived from clones of mouse genes was used to evaluate sensitivity. TaqMan-based PCR was perfromed to evaluate performance.

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The Rat Expression Set 230 incorporates the same expertise that was utilized for the design and performance of the GeneChip Human Genome U133 Set. For the design, genomic sequences were used to verify sequence selection, orientation, and the quality of sequence clustering. Additionally, clustering information from UniGene, build 99, was used with primary sequences and annotation information combined from a large variety of public databases to provide a more complete and accurate starting sequence data set.

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FS450_0004 when using the Hybridization, Wash and Stain Kit.

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The hybridization volume required is 200 µL. The total fill volume of the cartridge is 250 µL.

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Two arrays are in the set.

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The Rat Expression Set 230, consisting of two GeneChip arrays, contains over 31,000 probe sets representing more than 30,200 transcripts and variants, including over 28,000 well substantiated rat genes.

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