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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

Can samples be re-hybridized for CytoScan arrays?

Answer

No, this has not been validated at this time.

Answer Id: E13984

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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 until you are ready to wash them.

Answer Id: E13985

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Product FAQ

How long can CytoScan arrays filled with holding buffer be stored before scanning?

Answer

After the washing and staining step, arrays can be stored for up to 24 hours at 4 degrees C before scanning.

Answer Id: E13986

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Product FAQ

Are there any shutdowns run after bleaching the fluidics station when working with the CytoScan arrays?

Answer

Yes, it is recommended to run two water shutdown protocols after bleaching the fluidics station.

Answer Id: E13987

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Product FAQ

How does someone export LogRatios for the whole genome?

Answer

They can export the Whole Genome View as a PNG file. To do this, click on File > Export window PNG.

Answer Id: E14003

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Product FAQ

What is the array format for the CytoScan HD Array?

Answer

CytoScan HD Array uses a 49 format and a 5-μm feature size.

Answer Id: E13988

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Product FAQ

How do I unzip the array library file if I have to install it manually?

Answer

Right click the zip folder and click extract all. They can also use an already installed software that unzips files (e.g., Winzip, 7-zip, or any other equivalent software). Browse to the location to save the folder and click Extract. Go to the folder to find the files.

Answer Id: E14004

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Product FAQ

If I have only between 100 ng and 1 μg of total RNA, which protocol would you recommend, the One-Cycle or the Two-Cycle cDNA Synthesis protocol?

Answer

Since we recommend that you choose one protocol consistently for all samples to be compared within the same study, the procedure you choose may depend on the amount of RNA obtained from the majority of the samples you plan on including in the entire study. If most of the samples fall into the 100 ng to 1 μg range, it is reasonable to use the Two-Cycle Target Labeling protocol for the whole set of experiments. [This answer refers to a product that has been discontinued.]

Answer Id: E14367

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Product FAQ

What is the array content for the CytoScan HD Array?

Answer

CytoScan HD Array covers both constitutional and cancer genes with:
Overall intragenic coverage at 1 marker/880 bases
ClinGen (previously CCG and ISCA) constitutional coverage at 1 marker/384 bases
Complete cancer gene coverage at 1 marker/553 bases
14,000 OMIM genes at 1 marker/723 bases
>36,000 RefSeq genes at 1 marker/880 bases
Backbone (non-gene) coverage at 1 marker/1,737 bases across genome for breakpoints Overall (gene and non-gene backbone) coverage at 1 marker/1,148 bases

Answer Id: E13989

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Product FAQ

What is the library file location for ChAS?

Answer

The library file location for ChAS 2.1 and above is C:\Affymetrix\ChAS\Library.

Answer Id: E14005

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Product FAQ

How do results from GeneChip miRNA Arrays compare to Affymetrix miRNA Array Plates?

Answer

When evaluating non-control probe sets common to both arrays, we observed very high signal and fold change correlation for GeneChip miRNA 3.0 Arrays compared to Affymetrix miRNA 3.1 Array Plates (Pearson correlation coefficients of 0.97-0.98 for signal correlation and Pearson correlation coefficients of 0.96-0.98 for fold change correlation).

Answer Id: E14204

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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

Which copy number analysis parameters are new or have changed in GTC 3.0.1?

Answer

One copy number analysis parameter-the Regional GC Correction-is new and is on by default. Another copy number analysis parameter, the default value for the Confidence Score Threshold, has been changed to 1.0. Finally, a parameter was changed for gender determination in the copy number Segment Reporting Tool. For chromosome Y in males, the upper bound for the mean copy number was changed to 1.3 (see page 263 in the GTC 3.0.1 User Manual).

Answer Id: E13690

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Product FAQ

How long does it take to scan an array?

Answer

It takes approximately 35 minutes to scan each Exon Array.

Answer Id: E13659

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