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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 required for processing and viewing CytoScan 750K Array CEL files?

Answer

CytoScan Array CEL files are processed and analyzed in the Affymetrix Chromosome Analysis Suite Software (www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-analysis-instruments-software-services/microarray-analysis-software/chromosome-analysis-suite.html). This is a free download from our website. For processing the CEL files, a 64-bit computer, with a minimum of 8 GB of RAM, is required. You can view your resulting CYCHP files on a 32-bit or 64-bit computer. For 32-bit computers, it is important to note that the minimum amount of RAM needed is 3 GB. The recommended system specifications are included in the Chromosome Analysis Suite User Manual (https://tools.thermofisher.com/content/sfs/manuals/ChAS_Manual.pdf).

Answer Id: E13900

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Product FAQ

Is it required that all my equipment is current on its calibration and maintenance status?

Answer

For successful execution of the CytoScan Assay, it is important that your equipment is properly maintained and calibrated per manufacturers’ specifications. Please assure that your centrifuges, pipettes, thermal cyclers, and Affymetrix equipment, including the 645 Hybridization Oven, Fluidics Station(s), and Scanner, have had their last recommended maintenance prior to running the assay. For lab equipment, it is typically a yearly calibration. For the Affymetrix equipment, there is typically a yearly preventative maintenance.

Answer Id: E13901

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Product FAQ

What is the hybridization time for CytoScan 750K Arrays?

Answer

The hybridization time is 16 to 18 hours. If you have a limited number of fluidics stations, you can stagger the hybridization process by two hours. For example, if you have only one fluidics station and eight arrays, you can start the hybridization for four arrays at one time, and then start the hybridization for the other four arrays two hours later. After 16 hours, you can place the first four arrays on the fluidics station, and then place the next four arrays on the fluidics station two hours later. Thus, all eight samples will have hybridized for 16 hours. Another option is to wash the first set of samples at 16 hours and the second set at 18 hours.

We do not recommend staggering more than three wash/stain cycles in an 8-hour workday. Please consult your local Field Application Specialist for more details on the hybridization process.

Answer Id: E13919

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Product FAQ

What sample types are validated on the CytoScan 750K Array?

Answer

The CytoScan 750K Array has been validated with blood and cell line samples.

Answer Id: E13902

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Product FAQ

What is the hybridization temperature and rotation speed for the CytoScan 750K Array?

Answer

The hybridization temperature is 50 degrees C. The rotation speed is 60 rpm.

Answer Id: E13920

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Product FAQ

How many freeze/thaw cycles are validated for the CytoScan Assay 24-Sample Kit?

Answer

The CytoScan Reagent Kit (Cat. No. 901808) is validated for five freeze/thaw cycles.

Answer Id: E13903

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Product FAQ

Can arrays be registered in batches in the Command Console Software?

Answer

Yes. Please see the demonstration in the training and tutorials (www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-analysis-learning-center/microarray-analysis-training.html) section of the website for additional information.

Answer Id: E14244

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Product FAQ

For the CytoScan 750K Array, can samples be re-hybridized?

Answer

No, at this time this has not been validated.

Answer Id: E13921

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Product FAQ

What is the throughput for the CytoScan Assay?

Answer

We recommend running 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: E13904

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Product FAQ

Can I use GCOS software for miRNA Arrays?

Answer

No, we recommend using AGCC Software.

Answer Id: E14081

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Product FAQ

Which files are required to use the Fluidics Station 450?

Answer

The fluidics scripts are required in order to run the Fluidics Station. Please see the demonstration in the training and tutorials (www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-analysis-learning-center/microarray-analysis-training.html) section of the website for additional information.

Answer Id: E14245

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Product FAQ

Where can I find the Affymetrix sub-cluster information?

Answer

The Affymetrix sub-cluster information is available as an independent databank in the NetAffx Analysis Center under the "Affymetrix sub-cluster libraries group" (http://www.affymetrix.com/analysis/index.affx#1_1).

Answer Id: E13471

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Product FAQ

After hybridization, how long can the CytoScan 750K arrays be stored before washing and staining?

Answer

Arrays must be put onto the fluidics station immediately after removal from the hybridization oven. Do not remove arrays from the oven until you are ready to wash them.

Answer Id: E13922

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Product FAQ

What is CytoScan Cytogenetics Suite?

Answer

CytoScan Cytogenetics Suite consists of CytoScan arrays and CytoScan Reagent Kit, GeneChip Command Console Software (AGCC), and Chromosome Analysis Suite (ChAS). It enables the performance of high-resolution, genome-wide DNA copy number analysis and also provides genotyping information for the detection of copy neutral loss/absence of heterozygosity (LOH/AOH), which can be used to detect uniparental isodisomy (UPD). The combination of high-resolution DNA copy number data and the ability to detect gains, losses, and UPDs on a single array makes CytoScan Cytogenetics Suite ideal for cytogenetics studies.

Answer Id: E13939

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