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Product FAQ

What are the GeneChip Operating Software (GCOS) and GCOS Server Software (GCOS Server) products?

Answer

The GeneChip Operating Software (GCOS) is an operating system software that controls our instruments, acquires data, and executes gene expression analysis. In addition, GCOS contains an embedded database that manages both experiment information and data. Stratagene Array Assist Lite, Affymetrix GeneChip Sequence Analysis Software (GSEQ), Affymetrix GeneChip Genotyping Analysis Software (GTYPE), Affymetrix GeneChip Targeted Genotyping Analysis Software (GTGS) use data from the GCOS Database for gene expression cluster/statistical analysis, sequencing analysis and genotyping data analysis, respectively.

GCOS desktop version (client) can be conveniently upgraded to GCOS Server. With GCOS Server, customers benefit from increased systems flexibility, streamlined user interface integration, enhanced automation, and robust data handling and security. Using either an Oracle or SQL based server, researchers can perform a variety of data management tasks and data queries. Plus, extensive security features are available to allow users secure access to their data.

Answer Id: E13556

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Product FAQ

What is the recommended genomic DNA extraction methods used for the CytoScan assay?

Answer

Both blood and cell line sample sources have been tested with the CytoScan assay.
Methods that include boiling or strong denaturants are not acceptable because the DNA would be rendered single-stranded. Genomic DNA extracted using the following methods have been tested at ThermoFisher Scientific:

QIAGEN - Gentra Puregene Kit
5 PRIME - PerfectPure DNA Blood Kit
The CytoScan assay requires genomic DNA concentration >50 ng/µL. Therefore, the elution volumes for each of the kits will need to be adjusted accordingly to achieve the desired concentration.

Answer Id: E13950

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Product FAQ

I have lost my registration card for my Affymetrix software, what do I do?

Answer

Send an e-mail to techsupport@thermofisher.com requesting an e-registration form. After you complete the registration form and send it in to us, we will verify your software status and send you a new license.

Answer Id: E13616

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Product FAQ

Is there a genetic map and other SNP annotations with the Mapping arrays?

Answer

Yes, there is a variety of SNP annotations that are available through the NetAffx Analysis Center, including deCode and Marshfield genetic maps, allele frequency in three populations, chromosome, physical position, cytoband, and nearest genes.

Answer Id: E13703

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Product FAQ

How many freeze/thaw cycles are validated for CytoScan Reagent Kit (24 samples)?

Answer

CytoScan Reagent Kit (Cat. No. 901808) is validated for for 4 in-use freeze/thaw events but have to use the kit within a month (30 days) once opened even if they have not gone through 4 freeze-thaws.

Answer Id: E13951

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Product FAQ

I cannot see gene descriptions when I analyze the .dat file in Microarray Suite 4.x. How do I fix this?

Answer

First, verify that you are running the correct version of the Library Files (starting with November 2000), and that you are running Microarray Suite version 4.0.1 (required). If these versions are correct and you still encounter the problem, then there is, most likely, something wrong with the Microsoft Data Engine (SQL Manager). Contact us by e-mail at techsupport@thermofisher.com.

Answer Id: E13617

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Product FAQ

When should 500K enzymes be vortexed?

Answer

The enzyme alone should never be vortexed. The final cocktail, when specified, can be vortexed.

Answer Id: E13704

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Product FAQ

What is the NetAffx Analysis Center?

Answer

The NetAffx Analysis Center is the most comprehensive resource of integrated array contents and functional annotations available. The flexible query capabilities provided help you retrieve biological information for specific probe sets. Please read our Analysis Center tutorial for more information (http://www.affymetrix.com/analysis/index.affx#1_1).

Answer Id: E13455

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Product FAQ

Are individual genotypes generated from the CytoScan arrays?

Answer

Yes, genotypes can be generated in ChAS. The software uses BRLMM for genotyping, which uses a Bayesian model based on prior clusters. This product is not intended for genome-wide association studies.

Answer Id: E13998

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Product FAQ

How many samples should be processed at a time using the CytoScan assay?

Answer

It is recommended to run no more than 24 samples at a time. The assay is a four-day protocol; however, the technician can use an optional three-day protocol after becoming comfortable with the assay.

Answer Id: E13952

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Product FAQ

I can see the gene descriptions when I am logged on to the system with administrative rights, but I cannot see them when I am logged on as a normal user. How do I fix this?

Answer

This situation is most likely a permissions issue with the SQL Database. At the Start menu, open the Run menu, and run "regedt32". Once in the regedt32 window, select the "Software" option, then select "Affymetrix", "GeneChip", and "Database". With "Database" highlighted, select "Permissions" from the "Security" menu. Double-click on the user name, and select "Full Control (All)".

Answer Id: E13618

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Product FAQ

Are mitochondrial RNAs represented on this GeneChip Human Exon Array?

Answer

Based on mitomap, approximately 87 exons from the mitochondrial transcriptome are represented on this array.

Answer Id: E13554

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Product FAQ

Can the Axiom Genome-Wide BOS 1 Array Plate be used for copy number analysis?

Answer

There are no copy number probes on the array. However, measuring copy number variation (CNV) in the bovine genome can be performed using a custom whole-genome sampling assay design (a cartridge-based SNP Array 6.0 genotyping assay).

Answer Id: E14036

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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

When using the GeneChip Hybridization, Wash and Stain kit, I usually put wash buffer A on the array after I remove the hyb cocktail. The protocol says to add Array Holding Buffer. What should I do?

Answer

We recommend using the Array Holding Buffer supplied with the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

Answer Id: E14072

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