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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 I use glycogen as a carrier during my RNA extraction for microarray analysis?

Answer

We don't recommend that you use glycogen as a carrier since it is often contaminated with nucleic acids, sometimes has RNases, and can interfere with enzymes.

Answer Id: E14307

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Product FAQ

Why is it not necessary to run a globin reduction when using the Affymetrix WT assays?

Answer

We do not avoid globin through primer design for the GeneChip microarrays. All our assays label and/or amplify globin RNA and the amplified globins hybridize and generate array signals. However, our WT assays generate DNA as hybridization targets, which allow for the generation of strong signals of target transcripts even in the presence of globins.

Answer Id: E14308

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Product FAQ

What other reagents are required for the CytoScan Assay?

Answer

The CloneTech Titanium Taq PCR Kit (300 reactions, Cat. No. 639240 or 400 reactions, Cat. No. 639243) and absolute ethanol (Sigma Cat. No. 459844) are also required. All other reagents are included in the CytoScan Reagent Kit.

Answer Id: E13905

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Product FAQ

What does the percentage of aberrant cells mean?

Answer

This represents the percentage of aberrant cells in a sample:

When reported as “N/A,” it means that the percentage of aberrant cells could not be estimated.
When reported as a percentage (e.g., 60%), it means that 60% of the cells were aberrant.

Answer Id: E13859

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Product FAQ

Will high amounts of ribosomal RNA (rRNA) within a sample cause random primer amplification?

Answer

Our array biochemistry has been tailored to minimize the amplification of rRNA. We cannot disclose the specific mechanisms that are used. Additionally, cross-hybridization signal is reduced through our development of assay conditions that take advantage of the thermodynamic differences between labeled RNA targets and labeled cDNA targets that are hybridized to microarrays with attached DNA probes.

Answer Id: E14309

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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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Product FAQ

How long will it take for me to analyze the data for the GeneChip Exon Arrays?

Answer

Normalization of .cel files takes 1-3 minutes and generation of DABG and PLIER probe set level summaries takes about 40 minutes per .cel file. Further downstream analysis will depend on which data analysis techniques are being applied.

Answer Id: E13532

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Product FAQ

What is the expected length of the fragmented DNA target?

Answer

On a Bioanalyzer, the fragmented single-stranded DNA target should have a peak centered around 40 to 70 bases with the majority of the fragments ranging from 20 bases to 200 bases.

Answer Id: E13650

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Product FAQ

Can I use reagents from the Affymetrix SNP 6 Core Reagent Kit in the CytoScan Assay?

Answer

No. The CytoScan Assay has been optimized for performance with the CytoScan Reagent Kit, which is therefore required.

Answer Id: E13906

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Product FAQ

How long can I store a eukaryotic hybridization cocktail after the first hybridization for GeneChip Expression Assays?

Answer

Assuming that there is no RNase contamination, a cRNA hybridization cocktail can be stored for at least one year at -80 degrees C with no loss of sensitivity. The fact that the cRNA has been fragmented prior to the first array hybridization, reduces the risk of additional subsequent degradation.

Answer Id: E13587

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Product FAQ

How is fold change calculated in TAC?

Answer

Fold change is a number describing how much the signal changes from an initial condition group to a final condition group. These changes are represented in linear space. There are a couple of ways to describe fold change. One way a user might calculate this is to simply divide Sample A by Sample B and asses the result.

For example:
Array 1: Gene X - 1000 Gene Y - 5000 Gene Z - 500
Array 2: Gene X - 10000 Gene Y - 1000 Gene Z - 500
If comparing Array 1 vs Array 2: Gene X: 1000 / 10000 = 0.1 Gene Y: 5000 / 1000 = 5 Gene Z: 500 / 500 = 1
The way TAC displays fold change is to use the straight fold-change value if it is greater than or equal to 1.0 or display (-(1/fold change)) for values between 0 and 1. Let's look at the example above in TAC format:
Again, comparing Array 1 vs Array 2: Gene X: 1000 / 10000 = 0.1, so (-(1/0.1)) = -10 Gene Y: 5000 / 1000 = 5 Gene Z: 500 / 500 = 1
If doing the comparison the other way (Array 2 vs Array 1): Gene X: 10000 / 1000 = 10 Gene Y: 1000 / 5000 = 0.2 (or in TAC, (-(1/0.5)) = -5 Gene Z: 500 / 500 = 1

Answer Id: E14325

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Product FAQ

How does the Genome-Wide Human SNP 5.0 assay work?

Answer

Total genomic DNA (500ng) is digested with Nsp I and Sty I restriction enzymes and ligated to adaptors that recognize the cohesive four basepair (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 activated beads. The amplified DNA is then fragmented, labeled, and hybridized to a Genome-Wide Human SNP 5.0 Array.

Answer Id: E13740

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Product FAQ

Under what conditions can TuScan estimate the percentage of aberrant cell fraction?

Answer

This is possible when:

The tumor is nearly homogeneous (i.e., it has a major dominant clone), and the percentage of aberrant cell fraction is 40% or higher.

Answer Id: E13860

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Product FAQ

What is Vial 3, ATP Mix in the FlashTag labeling kit?

Answer

Vial 3 contains 10mM ATP.

Answer Id: E14059

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