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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

How long can the labeled products be stored at -20 degrees C?

Answer

The labeled products can be stored at -20 degrees C for no more than 10 days.

Answer Id: E13981

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Product FAQ

What is the hybridization time for CytoScan arrays?

Answer

The hybridization time is 16-18 hrs. If there are a limited number of fluidics stations, the hybridization process can be staggered by two hrs. For example, if there is only one fluidics station and eight arrays, the hybridization for four arrays can be started at one time, and then the hybridization for the other four arrays started two hrs later. After 16 hrs, the first four arrays can be placed on the fluidics station, and then the next four arrays placed on the fluidics station two hrs later. Thus, all eight samples will have hybridized for 16 hrs. Another option is to wash the first set of samples at 16 hrs and the second set at 18 hrs. It is not recommended to stagger more than three wash/stain cycles in an eight-hour workday. Please consult technical support at techsupport@thermofisher.com for more details on the hybridization process.

Answer Id: E13982

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Product FAQ

How often is data updated on NetAffx Analysis Center?

Answer

NetAffx Analysis Center contains both public and Affymetrix-generated data. Unless otherwise noted, public data representations are updated once every quarter (http://www.affymetrix.com/analysis/index.affx#1_1). Because we have considerable control over the proprietary internal data, we will keep you informed as new data and databanks become available.

Answer Id: E13460

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Product FAQ

What are some possible reasons for relatively lower 5.8S rRNA signals?

Answer

Less total RNA was loaded on those arrays
Those RNA samples were a little degraded
Those RNA samples were not human (even mouse would have lower signal intensity - homology is not perfect to human)
Those RNA samples were significantly enriched for 22mer / microRNA, removing the 5.8S rRNA which is around a 150mer

Answer Id: E14088

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Product FAQ

What are the two versions of Command Console Software?

Answer

We offers Standalone and Workgroup Editions of Command Console Software.

Answer Id: E14262

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Product FAQ

What can cause waviness SD failures when using the CytoScan Assay?

Answer

Waviness SD failures can be caused by degraded DNA, an incompatible sample type, or a sample-specific effect. See the CytoScan Assay User Manual (Cat. No. 703038, https://tools.thermofisher.com/content/sfs/manuals/cytoscan_assay_user_manual.pdf) and the Chromosome Analysis Suite User Manual (Cat. No. 702943) for more information.

Answer Id: E13935

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Product FAQ

After hybridization, how long can CytoScan 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 you are ready to wash them.

Answer Id: E13985

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Product FAQ

How do I learn more about the databases supported by the NetAffx Analysis Center?

Answer

Our Database Information Resource describes the functions and contents of the various databases used in the Analysis Center. Additionally, you can use the hyperlinks of the databases listed in the "top page" of the Analysis Center to obtain summaries of the databases.

Answer Id: E13461

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Product FAQ

Should I disregard all array data for probes that are not the same species as my RNA sample?

Answer

Most researchers eliminate the irrelevant species from analysis, because the extra data can be cumbersome. However, looking at multi-species probes may provide an increased confidence in the data. We typically observe a clustering of cross-species miRs that are identical, or nearly identical.

Answer Id: E14089

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Product FAQ

How are the new Command Console file formats better than those for GCOS?

Answer

1) Sample information is now stored in the sample file (ARR) that uses an industry-standard XML formatted file, enabling software packages outside of Command Console Software to easily access sample information.
2) File relationships (ARR/DAT/CEL/CHP) are now independent of file name, enabling users to rename and move files yet still retain parental lineage between the files. Contact the Affymetrix Developers' Network for more on technical aspects of Affymetrix files.

Answer Id: E14224

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Product FAQ

Can I perform the GeneChip Globin-Reduction kit protocol with less than 5 µg after concentration total RNA starting material?

Answer

The globin reduction method is optimized for use with 5 µg of total blood RNA. Starting with less than 5 µg is possible, but will lead to lower cRNA yields potentially leaving the user with insufficient material for hybridization.

Answer Id: E13487

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Product FAQ

What is the Command Console Standalone Edition?

Answer

The Standalone Edition is the desktop version of Command Console Software and is similar to GCOS workstation. Command Console Standalone has a web interface that provides sample registration, data organization, and administrative functionality. The standalone version is only accessible from the local computer and does not support remote connections. However, Command Console Standalone can use shared network storage to share data with other standalone workstations via the file system.

Answer Id: E14263

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Product FAQ

How are the 3' IVT Express kits shipped and what are the storage conditions?

Answer

The kits are shipped on dry ice, and are recommended to be stored at -20 degrees C. [This answer refers to a product that has been discontinued.]

Answer Id: E14354

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Product FAQ

Are individual genotypes generated on the CytoScan 750K Array?

Answer

Yes, genotypes can be generated in the Chromosome Analysis Suite (ChAS 3.3) Software. 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: E13936

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