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查看更多产品信息 511001 - FAQs (511001)
14 个常见问题解答
In Microarray Suite, click on the tools button on the menu bar. Select Analysis Settings, then Expression to open a dialog box. Chose the Mouse 430A or Mouse 430B probe array type from the dropdown list at the top of the dialog box. Now, select the Scaling tab. Click the radio button labeled Selected Probe Sets. To create a normalization mask file using a subset of these normalization genes, click Create/Open button. Give the new mask file a name and click open. Next, select the probe sets to use in the normalization from the exclude list on the left and once highlighted click the include button to move them to the include list on the right. Then click OK to return to the Expression Analysis Settings dialog box. Now you can use the browse button to select the mask file to use in the normalization and set the target intensity for your analysis.
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In Microarray Suite, click on the tools button on the menu bar. Select Analysis Settings, then Expression to open a dialog box. Chose the Mouse 430A or Mouse 430B probe array type form the dropdown list at the top of the dialog box. Now, select the Scaling tab. Click the radio button labeled Selected Probe Sets and enter the desired Target Signal in the open box. To scale to the normalization genes, click on the Browse button, select the appropriate mask file (MOE430Anorm.msk or MOE430Bnorm.msk) and click Open to return to the Expression Analysis Settings dialog box and click the OK button.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
A candidate list of probe sets was obtained in collaboration with an external site based on a large number of tissue samples run on MG-U74v2 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 Mouse 430A 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, 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 Mouse 430A and Mouse 430B 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 Mouse Genome Sequencing Consortium (MGSC) version 3 assembly was used to design the Mouse 430 set. 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 Mouse 430 set is not a genome tiling product, but rather an mRNA expression product; thus the entire mouse 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 Mouse 430, are available through the Support by Product page.
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The probes on the Mouse Set 430 are designed to detect the anti-sense strand of the gene of interest, and these probe sets are annotated with the "_at" extension. The primary goal in probe selection is to select a probe set unique to a 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 Mouse Expression Set 430 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 Mouse 430 and MG-U74v2 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 30 prelabeled spikes derived from clones of mouse genes was used to evaluate sensitivity. Approximately 30 transcripts were evaluated both by array and by real-time quantitative PCR (TaqMan) to evaluate performance.
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The Mouse Expression Set 430 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 107, 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 . The fluidics protocols are loaded when the library files for a given probe array type are installed.
Additional information, including lists of steps in the fluidics protocols, can be found in the GeneChip Expression Analysis Technical Manual (https://tools.thermofisher.com/content/sfs/manuals/expression_analysis_technical_manual.pdf).
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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 Mouse Expression Set 430, consisting of two GeneChip arrays, contains over 45,000 probe sets representing more than 39,000 transcripts and variants, including over 34,000 well substantiated mouse genes.
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