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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 does “low diploid flag” mean?

Answer

The algorithm identifies normal diploid markers in the cancer samples. This is particularly important in highly aberrant samples. The normal diploid markers are used to calibrate the signals so that a log2 ratio of 0 (e.g., copy number 2) is achieved. In about 2% of samples, the algorithm cannot identify a sufficient number of “normal diploid” markers, and no normal diploid calibration occurs. This event triggers “low diploid flag = YES.” In this case, the user needs to carefully examine the log2 ratios and verify that re-centering is necessary.

Answer Id: E13864

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Product FAQ

Can I create my own reference set?

Answer

We have not enabled the capability for customers to create their own reference sets. (This process requires careful sample selection and randomization.) Our universal reference has been developed to represent a wide variety of different samples and ages. The samples used in the reference set have been sourced from many different countries. In our beta tests, the universal reference has performed well in the following countries as of 09/29/2013: USA, UK, France, Germany, and Japan

Answer Id: E13865

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Product FAQ

How do the labels in the GeneChip IVT Labeling Kit work?

Answer

The IVT Labeling Kit contains a proprietary biotinylated nucleotide analog (patent pending). This analog is incorporated in the T7 RNA polymerase-mediated IVT amplification and labeling reaction as a pseudouridine reagent to generate cRNA targets.

Answer Id: E13612

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Product FAQ

How does the Affymetrix Mouse Diversity Genoytping Array assay work?

Answer

Total genomic DNA (500 ng) is digested with Nsp I and Sty I restriction enzymes and ligated to adaptors that recognize the cohesive 4 base pair (bp) overhangs. All fragments resulting from restriction enzyme digestion, regardless of size, are substrates for adaptor ligation. A generic primer that recognizes the adaptor sequence is used to amplify adaptor-ligated DNA fragments. PCR conditions have been optimized to preferentially amplify fragments in the 200 to 1,100 bp size range. PCR amplification products for each restriction enzyme digest are combined and purified using polystyrene beads. The amplified DNA is then fragmented, labeled, and hybridized to a Mouse Diversity Genotyping Array.

Answer Id: E14154

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Product FAQ

What is the difference between OncoScanCancerGeneOnly.r1 and OncoScanGeneBoundaries.r1?

Answer

OncoScanGeneBoundaries.r1 lists the approximately 900 OncoScan cancer genes and includes greater than 10 kb on each side of the gene. OncoScanCancerGeneOnly.r1 lists the same approximately 900 OncoScan cancer genes using the start and stop positions of the gene (no additional 10 kb on each side of the gene).

Answer Id: E13866

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Product FAQ

How were SNPs selected for the Axiom Genome-Wide BOS 1 Array?

Answer

SNPs were selected to represent polymorphisms from a comprehensive set of commercially important breeds of dairy and beef cattle from both Bos indicus and Bos taurus. Our primary goal was to obtain high levels of genetic coverage. SNP pairwise linkage disequilibrium (LD) values (r2) were calculated to identify SNPs in strong LD. Then we selected the fewest number of SNPs to cover the known genetic variation for each breed we prioritized (first five breeds in Table 1). After SNPs were selected for optimal genetic coverage, the distances between the selected SNPs were calculated, and inter-SNP gaps filled (starting with the largest) by selecting polymorphic SNPs from the five major breeds: Holstein, Angus, Nelore, Jersey, and Fleckvieh.

Answer Id: E14033

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Product FAQ

The recommended starting amount of total RNA for the One-Cycle protocol has been reduced from 5 µg to 1 µg. Do you have any data to support that the procedure works well with the reduced amount of starting material?

Answer

Studies were conducted in-house to compare the data obtained from 1 µg vs. 5 µg of starting total RNA, and the array results were highly concordant with respect to detection sensitivity (percent Present call) and reproducibility (Signal correlation, Absolute Call concordance). However, subtle differences were observed. Therefore, for best comparability of results, it is generally recommended to use the same amount of starting RNA in studies where the data are intended to be directly compared.

Answer Id: E13613

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Product FAQ

For the Affymetrix Mouse Diversity Genoytping Array, how much and what quality of genomic DNA is required to perform the assay?

Answer

The assay requires 500 ng of high-quality, double-stranded genomic DNA that is not highly degraded. Genomic DNA must be free of PCR and other enzymatic inhibitors such as high salt, heme, and EDTA. For details about general assay requirements for genomic DNA, please refer to Chapter 3, page 19 of Affymetrix Genome-Wide Human SNP Nsp/Sty 6.0 User Guide (Cat. No. 702504). We have tested a variety of extraction and purification methods as well as cleanup procedures that are also listed in this user guide.

Answer Id: E14155

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Product FAQ

What data files are produced during the assay and analysis process?

Answer

These data files are produced that are key to the process:

ARR file - This file includes sample information.
AUDIT file - This file is a log of the sample history.
DAT file - This file is the raw data from the scanner.
CEL file - This file is the gridded and processed data.
xxCHP file - This file is the output of ChAS 3.1 and contains all of the analysis data.
CHPCAR file - This file stores user-annotated calls, interpretations, and modifications made to CHP file segment data (ChAS v2.0 and higher).

Answer Id: E13867

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Product FAQ

How can I view the histogram data in ChAS 3.1?

Answer

You must be logged into the ChAS database (ChAS DB) to view histogram data. The histograms are only available for NetAffx genomic annotation files for genome build Hg19. The browser produces an error message if you try to load Hg19-based histograms while an Hg18-based NetAffxGenome Annotation is currently displayed.

Answer Id: E13883

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Product FAQ

After performing globin reduction on PAXgene Blood RNA using the GeneChip Globin-Reduction Kit, do I get an equivalent expression profile to the same sample when starting with RNA isolated using an erythrocyte lysis method?

Answer

No. The resulting blood cell fraction obtained using an RNA isolation method that includes erythrocyte lysis overlaps only in part with the cell population represented in RNA isolated from whole blood. The globin reduction procedure is designed to improve GeneChip assay sensitivity by eliminating amplification and labeling of the very abundant globin transcripts found in red blood cells. However, although these transcripts are present at high levels, they constitute only a very small number of the total different transcripts contributed to the sample by this cell population. Therefore, even after globin reduction, RNA isolated from whole blood has additional transcripts not found in RNA isolated by erythrocyte lysis thereby resulting in differences in the expression profiles obtained using these different methods.

For more detailed information on cell fractions represented following different blood collection or RNA isolation methods, please refer to the technical note entitled "Globin Reduction Protocol: An analysis of blood processing methods to prepare samples for GeneChip expression profiling" (http://media.affymetrix.com/support/technical/technotes/blood_technote.pdf).

Answer Id: E13492

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Product FAQ

What is the nature of specificity of the probes included in the HG-U133 Set?

Answer

The probes on the HG-U133 Set are designed to detect the anti-sense strand of the gene of interest, and these probes are annotated with the "_at" extension. The primary goal in probe set selection is to select a probe set unique to a single transcript or common among transcripts from the same gene.

Often, it is not possible to select a probe set that is unique to a single transcript because multiple transcript variants share common sequence. Such probe sets are annotated with the "_s_at" extension. Occasionally, it is not possible to select a unique or shared probe set. Such probe sets are annotated with the "_x_at" extension. For more information, please review the _s_at and _x_at_ probe set descriptions.

Please note: There are no "_f_at", "_g_at", or "_r_at" probe sets in the HG-U133 design, as opposed to the HG-U95 Array design. This is because the nonunique probe set types were simplified and adjusted to account for improvements due to improved probe selection rules.

Answer Id: E13770

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Product FAQ

In the Command Console Software, what are templates?

Answer

Templates are used to store groups of attributes and their controlled vocabularies. Controlled vocabularies can be used to enforce consistent metadata within studies.

Answer Id: E14237

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Product FAQ

How was genetic coverage calculated for the Axiom Genome-Wide BOS 1 Array?

Answer

Genetic coverage was calculated based on SNP pairwise LD (r2) results obtained from genotype data of reasonably unrelated samples within each breed of interest. The default r2 threshold for genetic coverage was 0.8. Unless otherwise specified, all SNPs with r2 results for a given breed are included in the target coverage set. This set includes all SNPs that are converted in the screen and have polymorphic genotype data for the breed of interest. For breeds for which bovine HapMap genotype data were available for enough of the samples used in the screen, HapMap SNPs with polymorphic genotypes were also included in the target coverage set.

Answer Id: E14034

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