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Product FAQ

What is the array content for the CytoScan 750K Array?

Answer

The CytoScan 750K Array covers both constitutional and cancer genes with:

-Overall intragenic coverage at 1 marker / 1,737 bases
-ISCA constitutional coverage at 1 marker / 1,099 bases
-Complete cancer gene coverage at 1 marker / 1,269 bases
-12,000 OMIM genes at 1 marker / 2,204 bases
->36,000 RefSeq genes at 1 marker / 1,737 bases
-Backbone (non-gene) coverage at 1 marker / 6,145 bases across genome for breakpoints
-Overall (gene and non-gene backbone) coverage at 1 marker / 4,127 bases

Answer Id: E13927

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Product FAQ

Why does the alignment position detected by Probe Match tool differ from the probe interrogation position information associated with the probe sequence record?

Answer

The probe interrogation position, provided with the probe sequence information, indicates the base position on the consensus/exemplar sequence where the central base of the probe aligns (the 13th base of a 25mer probe). The position information generated by the Probe Match tool is strictly based on the alignment against the query (input) sequence. Because the consensus/exemplar may not be co-linear with your input sequence, the probe interrogation position in a probe sequence record may not match the output from the Probe Match tool.

Answer Id: E13638

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Product FAQ

How many and what species are not detected by the Axiom Microbiome Array?

Answer

81 species are not detectable on Axiom Microbiome Array. For a complete list of species not detected, please contact the Technical Support Team.

Answer Id: E14305

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Product FAQ

Will the Affymetrix Mouse Diversity Genoytping Array be available in plate format?

Answer

Content found on the Mouse Diversity Genotyping Array is so comprehensive that it will not fit on the format required for array plates.

Answer Id: E14152

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Product FAQ

I have noticed that the allele peaks calculation (ChAS 2.1 or below) is now called allele difference (ChAS 3.1 and above). Does this mean that the algorithm changed?

Answer

No, it is solely a name change for consistency.

Answer Id: E13887

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Product FAQ

Do I need to apply the high-resolution scanning patch for the HG-U133 2.0 Arrays?

Answer

Below is a list of circumstances and clarification regarding whether or not the high resolution scanning patch needs to be applied. Keep in mind that the high resolution scanning patch must only be applied on top of GCOS, not AGCC.

a. GeneChip Scanner 3000 (serial numbers 502xxxxx): The instrument service engineer has applied the high-resolution scanning patch to the computer that is controlling the GeneChip Scanner 3000 at installation, but not to the workstations or servers (see c and d below).

b. GeneChip Scanner 3000 (serial numbers 501xxxxx): The instrument service engineer will apply the high-resolution scanning patch to the computer that is controlling the GeneChip Scanner 3000 at the time of the upgrade, but not to the workstations or servers (see c and d below).

c. Analysis workstations and clients: You must apply the high-resolution scanning patch to GCOS analysis workstations.

d. GCOS Server upgrade: Your GCOS database administrator or an Affymetrix Software Support Engineer needs to apply the high-resolution scanning patch in coordination with the upgrade of server to GCOS.

e. Installation of library files post scanner installation or upgrade: The high-resolution scanning patch must be reapplied following the installation of library files for arrays that precede the HG-U133A 2.0 and HG-U133 Plus 2.0 Arrays. The HG-U133A 2.0 and HG-U133 Plus 2.0 library files are high-resolution-scanning ready. The error message "cannot read the parameters for probe array type from the database" appears when one tries to scan an array on a GeneChip Scanner 3000 high-resolution scanner when the high-resolution scanning patch has not been applied.

Answer Id: E13778

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Product FAQ

How were SNPs selected for the Axiom Genome-Wide BOS 1 Array?

Answer

SNPs were selected to represent polymorphisms from a comprehensive set of commercially important breeds of dairy and beef cattle from both Bos indicus and Bos taurus. Our primary goal was to obtain high levels of genetic coverage. SNP pairwise linkage disequilibrium (LD) values (r2) were calculated to identify SNPs in strong LD. Then we selected the fewest number of SNPs to cover the known genetic variation for each breed we prioritized (first five breeds in Table 1). After SNPs were selected for optimal genetic coverage, the distances between the selected SNPs were calculated, and inter-SNP gaps filled (starting with the largest) by selecting polymorphic SNPs from the five major breeds: Holstein, Angus, Nelore, Jersey, and Fleckvieh.

Answer Id: E14033

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Product FAQ

Do you have exon coverage in the high-resolution genes?

Answer

Yes, if using the Affymetrix defined workflow and depending on the size of the exon (our algorithm requires 20 contiguous markers to make a call). If using an “open” workflow, the user can define the number of probes they need to claim exon resolution.

Answer Id: E13856

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Product FAQ

Where can I get a list of miRNAs represented on Thermo Fisher Scientific miRNA Arrays?

Answer

You can get the list by downloading the annotation files that will be available on the website.

Answer Id: E14135

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Product FAQ

How do I know if my first-cycle IVT reactions have worked well?

Answer

After the first cycle of amplification, it is often possible to quantitate the cRNA yield at this stage. Routinely, 400 ng - 1 µg of cRNA can be obtained from 50 to 100 ng of starting material. However, it is difficult to use the cRNA yield as the only metric to determine the success of the assay. Therefore, it may be most informative to combine the results from the first-cycle IVT yield with the second-cycle IVT yield, as well as array-quality metrics and data on various positive controls, to obtain a comprehensive view of how the assay has proceeded. [This answer refers to a product that has been discontinued.]

Answer Id: E14369

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Product FAQ

Why is my favorite array not listed in the sub-cluster databank in the NetAffx Analysis Center?

Answer

Some array designs, such as the GeneChip Mu19K array, are based on the sequences in The Institute for Genomic Research (TIGR) (http://www.jcvi.org/cms/home/) databanks. Sub-cluster information for these probe arrays is considered TIGR's proprietary information and therefore cannot be distributed by Affymetrix.

Answer Id: E13474

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Product FAQ

What is the purpose of the mPCR step in the DMET Plus assay?

Answer

The mPCR step allows for genes that have pseudogenes or other regions of high homology to be amplified for accurate genotyping. The mPCR is designed to preferentially amplify the real gene of interest.

Answer Id: E14300

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Product FAQ

Which assay do you recommend for use with Affymetrix miRNA Array Plates?

Answer

We only support use of the Affymetrix FlashTag Biotin HSR RNA Labeling Kit for preparing targets to be applied to GeneChip miRNA Array .

Answer Id: E14110

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Product FAQ

How do I limit an analysis in the TAC software to my genes of interest?

Answer

In the TAC software, you can filter the list of results by a list of gene symbols. This will also limit the hierarchical clustering of your expression data to the gene symbols found on your list. To do this, proceed with your analysis as you normally would. Once the results are returned, in the Table tab, you right click on the Gene Symbol column and choose the Filter option. A pop up will then appear allowing you to apply the filter logic. To filter on a list of Gene Symbols, select either the ‘In List' or ‘Not In List' option, as it pertains to your query. The Edit List window will appear, allowing you to type or paste in gene symbols. These must be separated by comma, semi-colon, or line breaks to be recognized properly by the software. Please also note that we use the official gene symbol determined by the NCBI Gene database. If your gene symbol of interest does not appear to function properly, please confirm that it is the official gene symbol by consulting the NCBI Gene database website.

Answer Id: E14332

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Product FAQ

In miRNA QC tool, how is the P-value calculated?

Answer

The p-value is calculated using the 4 probe replicates for each miRNA, and the corresponding variance for each set. Detection means: probe performance/detection using an algorithm and comparing to background.

Answer Id: E14085

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