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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

Which copy number workflows for the 100K Set/500K Array Set are supported in GTC 4.2?

Answer

The following paired and unpaired analysis workflows are supported for the 100K Set/500K Array Set:
-Copy number (CN)
-Loss of heterozygosity (LOH)
-Copy number segment reporting
-Custom region copy number segment reporting

-Paired CN Analysis is used to compare two samples from the same individual to look for copy number differences in different types of tissues.
-Unpaired CN Analysis is used to compare sample files to a set of reference files.

Answer Id: E13688

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Product FAQ

Which copy number workflows for the SNP Array 6.0 are supported in GTC 4.2?

Answer

GTC 4.2 can be used to perform the following copy number analyses for the SNP Array 6.0:

-Copy number (CN)
-Loss of heterozygosity (LOH)
-Copy number segment reporting
-Custom region copy number segment reporting

There are two options for copy number analysis workflows on the SNP Array 6.0:

-CN/LOH Reference Model File Creation and Analysis (Batch Sample Mode)
-CN/LOH Analysis with a Previously Created Reference Model File (Single Sample Mode)

Answer Id: E13689

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Product FAQ

Does GTC 4.2 provide a reference model file for copy number analysis?

Answer

GTC 4.2 provides a reference model file for the SNP Array 6.0, generated from the 270 HapMap data set. 100K Set and 500K Array Set 270 HapMap data can be used to generate reference sets for those probe array types.

Answer Id: E13694

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Product FAQ

What is the maximum number of freeze/thaw cycles recommended for the CytoScan Reagent kit?

Answer

The CytoScan Reagent kit has been validated for less than or equal to 5 freeze/thaw cycles.

Answer Id: E14279

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Product FAQ

How many genes and transcripts are represented on the arrays in the GeneChip Mouse Expression Set 430?

Answer

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.

Answer Id: E13716

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Product FAQ

Should I anticipate the same results using the Poly-A controls with all eukaryotic GeneChip expression arrays?

Answer

The Signal intensity representative data (globally scaled) shown in the package insert are typical results for the newest probe design from Affymetrix (3' AFFX-r2-Bs). These probe sets are available on catalog arrays including the GeneChip Human Genome U133, Mouse 430, and Rat 230 arrays.
However, with previous generations of probe sets, the Signal values observed may vary from those shown. Nevertheless, utilization of these controls still serves as a good indicator of the experimental process quality, low-end sensitivity, and assay dynamic range. Some of the arrays that have the older probe sets include the Drosophila Genome Array and Yeast Genome S98 Array.

Answer Id: E14379

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Product FAQ

Can I generate my own reference model files for SNP Array 6.0 copy number analysis?

Answer

Yes, you can generate your own reference model files for copy number analysis. A user-generated reference set may better account for laboratory bias and may therefore improve resolution. Reference sets should contain at least 44 samples. To obtain good data on the X and Y chromosomes, you should use a minimum of 15 files from female samples and 15 files from male samples to generate the reference model file.

Answer Id: E13695

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Product FAQ

How many arrays are in the GeneChip Mouse Expression Set 430?

Answer

Two arrays are in the set.

Answer Id: E13717

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Product FAQ

How does this kit perform with labeling kits other than those recommended in the Affymetrix protocols?

Answer

We have not tested the performance of this kit extensively with any other kits/protocols other than the Standard and Small Sample Target Labeling assays currently recommended by us. Therefore, we are not able to provide any sample data or support when this kit is used with any other procedures.

Answer Id: E14380

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Product FAQ

Can I export my data in text format?

Answer

Yes. With ChAS 3.1 and above, you can now export table data in word (docx), pdf, text, or transfer to clipboard. You can export graphic view data in pdf, docx, and png formats.

Answer Id: E13874

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Product FAQ

Which Affymetrix platforms support CNP analysis?

Answer

CNP analysis is supported in GTC 4.2 for the SNP Array 6.0.

Answer Id: E13696

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Product FAQ

Which type of freezer should be used to store CytoScan Reagent kit components that require -20 degrees C?

Answer

The reagents that require storage at -20 degrees C must not be stored in a frost-free freezer. The activity of the enzymes will be decreased.

Answer Id: E14280

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Product FAQ

Why do the pre- and post-PCR areas need to be separated?

Answer

The post-PCR lab contains amplicons, whereas the pre-PCR area should not. These amplicons can be inadvertently transferred back to the pre-PCR area, thus contaminating the lab and posing a contamination threat to all reactions set up in the pre-PCR lab. Because all samples are amplified using the same primers and adaptors, contaminating DNA can also be amplified.

Answer Id: E13961

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Product FAQ

What is the volume of hybridization cocktail for the GeneChip Mouse Expression Set 430?

Answer

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

Answer Id: E13718

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