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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 the array content for the CytoScan™ 750K Array?

Answer

The CytoScan™ 750K Array covers both constitutional and cancer genes with:

-Overall intragenic coverage at 1 marker / 1,737 bases
-ISCA constitutional coverage at 1 marker / 1,099 bases
-Complete cancer gene coverage at 1 marker / 1,269 bases
-12,000 OMIM genes at 1 marker / 2,204 bases
->36,000 RefSeq genes at 1 marker / 1,737 bases
-Backbone (non-gene) coverage at 1 marker / 6,145 bases across genome for breakpoints
-Overall (gene and non-gene backbone) coverage at 1 marker / 4,127 bases

Answer Id: E13927

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Product FAQ

How is the CytoScan™ assay different from the assay used with Affymetrix™ Genome-Wide Human SNP Array 6.0?

Answer

The CytoScan™ assay has significantly fewer pipetting steps and requires less hands-on time than the Genome-Wide Human SNP 6.0 assay. The CytoScan™ assay uses only the Nsp I restriction enzyme and has been optimized for cytogenetics applications. The CytoScan™ assay is not intended for genome-wide association studies.

Answer Id: E13958

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Product FAQ

How many SNP and CN probes are included on the CytoScan™ 750K Array?

Answer

The CytoScan™ 750K Array includes 200,000 genotype-able SNPs and 550,000 non-polymorphic probes.

Answer Id: E13928

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Product FAQ

How can I modify the mask or make my own that contains a subset of the normalization genes in the GeneChip™ Mouse Expression Set 430?

Answer

In Microarray Suite, click on the tools button on the menu bar. Select Analysis Settings, then Expression to open a dialog box. Chose the Mouse 430A or Mouse 430B probe array type from the dropdown list at the top of the dialog box. Now, select the Scaling tab. Click the radio button labeled Selected Probe Sets. To create a normalization mask file using a subset of these normalization genes, click Create/Open button. Give the new mask file a name and click open. Next, select the probe sets to use in the normalization from the exclude list on the left and once highlighted click the include button to move them to the include list on the right. Then click OK to return to the Expression Analysis Settings dialog box. Now you can use the browse button to select the mask file to use in the normalization and set the target intensity for your analysis.

Answer Id: E13732

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Product FAQ

Can I buy just the reagents or arrays alone instead of the CytoScan™ Reagent Kit?

Answer

No, the reagents and arrays are sold as bundles for 24 reactions (Cat. No. 901835)

Answer Id: E13959

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Product FAQ

How long does the CytoScan™ 750K Array take to scan?

Answer

Each array takes ~7 minutes to scan

Answer Id: E13929

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Product FAQ

Are there any transcripts represented exactly as they were on MG-U74v2?

Answer

The hybridization controls (bioB, bioC, bioD, cre), polyA+ controls (dap, lys, phe, thr and trp) and housekeeping (beta-actin, gapdh, transferrin receptor and pyruvate carboxylase) genes are represented by 20 probe-pair probe sets as on the MG-U74v2 Set. In addition, the hybridization controls and the majority of the polyA+ controls are also represented by 11 probe-pair probe sets.

The remaining probe sets representing mouse transcripts were selected based on more recent sequence information with improvements to sequence and probe selection methods. The new probe sets have 11 probe pairs, while MG-U74v2 probe sets have 16 probe pairs. Thus, probe sets representing similar transcripts will not be identical. The comparison spreadsheets (and associated instructions) available at Affymetrix.com will be useful tools to understand the relationships between the probe sets and the probe selection regions of these two array designs.

Answer Id: E13733

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Product FAQ

Do you have any specific recommendation on the type of non-stick tubes to use for diluting the Poly-A RNA Control Stock?

Answer

The following tubes were used in-house during product development of this Poly-A RNA Control Kit, and we have not tested any other tubes at this time:
Non-stick RNase-free 0.5 mL microfuge tubes, Ambion, cat #12350
Non-stick RNase-free 1.5 mL microfuge tubes, Ambion, cat #12450

Answer Id: E14385

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Product FAQ

What is the purpose of including a positive and negative genomic DNA control in each CytoScan™ assay, and what would be the passing and failing results for each control type?

Answer

Positive control: This sample has prior proven performance and represents a pristine sample, meeting all genomic DNA input requirements. The performance of this sample helps to assess the quality of the assay steps and final product. In troubleshooting cases, performance of this control sample versus that of non-control samples can help to parse out possible assay failure culprits.

Negative control: For this assay, the negative control is simply reduced EDTA TE Buffer and acts as a control for the process up to the PCR quantitation and PCR gel. If no smear is seen on the PCR gel, it is considered passing, indicating that there is no DNA contamination in any of the reagents that could lead to amplification of other targets. A failing result will have a smear in the PCR gel. Note that the presence of PCR primer dimers is expected.

Answer Id: E13960

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Product FAQ

What file sizes are associated with the CytoScan™ 750K Array?

Answer

The CEL file is ~46 MB, and the CYCHP file is ~33 MB.

Answer Id: E13930

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Product FAQ

What is the difference between a PSR and an Exon?

Answer

PSR is the smallest unit on the exon array for expression profiling and each PSR is represented by an individual probe set. In some cases, each PSR is also an exon; in other cases, due to variation in overlapping exon structures, the PSR can be a subset of the true biological exon. As a result, alternatively spliced exons from the same gene may overlap (i.e., alternative donor or acceptor site); however, PSRs have the property that they do not overlap each other in the genome space, except if annotations change with a newer version of the genome assemblies. In cases where multiple annotations infer different exon structures, that one exon cluster (a group of overlapping exons) will be divided into multiple PSRs. Therefore, in the final design, there are approximately 1,000,000 exon clusters represented by approximately 1,400,000 PSRs.

Answer Id: E13543

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Product FAQ

What sample types are validated on the CytoScan™ assay?

Answer

The CytoScan™ assay has been validated with blood and cell line samples.

Answer Id: E13947

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Product FAQ

What is the CytoScan™ HD Array content?

Answer

-CytoScan™ HD Array covers both constitutional and cancer genes with Overall intragenic coverage at 1 marker/880 bases
-ClinGen (ISCA) constitutional coverage at 1 marker/384 bases
-Complete cancer gene coverage at 1 marker/553 bases
-12,000 OMIM™ genes at 1 marker/659 bases
->36,000 RefSeq genes at 1 marker/880 bases
-Backbone (non-gene) coverage at 1 marker/1,737 bases across the genome for breakpoints
-Overall (gene and non-gene backbone) coverage at 1 marker/1,148 bases

Answer Id: E13833

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Product FAQ

Which fluidics protocol should I use when processing a Gene 1.0 ST Array?

Answer

FS450_00007 should be used when processing Gene 1.0 ST Array. Up-to-date fluidics scripts can be obtained from the website.

Answer Id: E14097

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