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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

Where can I find the high-resolution scanning patch for the Mouse 430 2.0 Arrays?

Answer

Please contact Technical Support to obtain the high-resolution scanning patch.

Answer Id: E13711

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Product FAQ

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

Answer

CytoScan™ 750K Array includes a total of 1.15 million probes: 1 probe per allele in triplicate for 200,000 SNP probes and 550,000 non-polymorphic probes.

Answer Id: E13837

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Product FAQ

How do you move the .cel files out of GCOS to be imported into Expression Console?

Answer

GCOS users must use DTT v1.1, using the Flat File option, to transfer files to be analyzed by the Expression Console software from the GCOS database to an independent folder.

Answer Id: E13538

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Product FAQ

For the CytoScan™ assay, can a different magnetic rack be used instead of the recommended MagnaRack™ magnetic stand?

Answer

Yes, the assay is currently validated for the following magnetic racks:
DynaMag™-2 Magnet (Cat. No. 123-21D)
MagnaRack™ (Cat. No. CS15000)

Answer Id: E13971

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Product FAQ

What are the assumptions you have used in estimating the concentrations in terms of complexity ratio of these control transcripts in a sample?

Answer

The concentrations in terms of complexity ratios are calculated based on the following assumptions:
Average transcript length = 2,000 bases
Average MW of a single base = 330 g/mole
mRNA constitutes approximately 2% of the total RNA sample

Answer Id: E14372

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Product FAQ

How much memory is needed to store the data from a single Mouse 430 2.0 Array?

Answer

A single Mouse 430 2.0 array generates approximately 130MB of data.

Answer Id: E13712

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Product FAQ

What software is available for analysis of the Genome-Wide Human SNP Array 6.0?

Answer

-Genotyping Console 2.1
-Algorithm Birdseedv2

Answer Id: E13755

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Product FAQ

What array software is available for genoytping, copy number analysis, and analysis for CytoScan™ Optima Suite?

Answer

All genotyping, copy number analysis, and analysis for CytoScan™ Optima Suite is done with ChAS 3.1. This product is not intended for genome-wide association studies

Answer Id: E13838

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Product FAQ

What kinds of annotation will be available for GeneChip™ Exon arrays?

Answer

-Information about the annotation types supporting each probe set
-Genome coordinates for all PSRs, probe sets, and probes
-Various quality information about the probe and probe sets (i.e., number of overlapping probes in a probe set)
-Some biological annotation (i.e., gene names)

Answer Id: E13552

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Product FAQ

Can I hybridize the DNA target to the HG-U133 arrays?

Answer

The WT Sense Target Labeling Assay is optimized to produce targets specifically for hybridization to the Exon Array type of design. The target is in the sense orientation and the GeneChip™ Human Genome U133 Plus 2.0 Array is designed to be compatible with anti-sense targets. Therefore, it is not recommended to mix and match the assays and the array types.

Answer Id: E13654

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Product FAQ

Two alternative splicing detection methods were described in the white papers on your web site. Are they related to the ANOSVA SVD algorithm that was published in Bioinformatics in 2005 by Cline, et al?

Answer

No, the methods in the white papers are not ANOSVA which was published in the paper referenced (http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/suppl_1/i107). One note about ANOSVA is that it was developed on a combination exon/junction array. Some preliminary work comparing ANOSVA and PAC (one of the two methods described in the white papers) on the exon array tissue panel suggests that the MiDAS and the robust PAC methods presented in the white papers are a better way to go.

Answer Id: E13539

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Product FAQ

What is the typical yield range from PCR product purification?

Answer

The minimum recommended yield is 2.5 μg/μL for a sample. Yields can range from 3.0-4.5 μg/μL, and the average yield for seven or more samples processed in a run (not including the negative control) should be greater than 3.0 μg/μL. If the average yield is below this, consult the troubleshooting section of the CytoScan™ Assay User Manual (Cat. No. 703038, https://tools.thermofisher.com/content/sfs/manuals/cytoscan_assay_user_manual.pdf).

Answer Id: E13972

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Product FAQ

Based on these assumptions, how did you calculate the concentrations in terms of complexity ratios from the starting concentrations of the poly-A RNA controls in the Poly-A Control Stock?

Answer

The concentrations of the poly-A RNA controls in the stock solution are as follows:
lys - 7.6 nM
phe - 15.2 nM
thr - 30.4 nM
dap - 114.0 nM

A complexity ratio is the ratio of the number of copies of poly-A control transcript to the total number of mRNA transcripts in the sample. Complexity can also be expressed as a ratio of molar amounts (since 1 mole contains 6.02 x 10^23 molecules). Here are the calculations for the 1:100,000 concentration in terms of complexity ratio for lys when spiked into 5 μg of starting total RNA:

Calculations for lys:
Stock concentration of lys: 7.6 nM (7.6 nmoles/L)
Total dilution in final input (from Product Insert): 1:10,000 (or (1:20) * (1:50) * (1:10))
Amount of diluted poly-A spike-in volume (from Product Insert): 2 μL (7.6 nmoles/L)*(1/10,000)*(1 L/1x10^6 μL)*(2 μL) = 1.52 x 10^-9 nmoles

Calculations for starting RNA:
Starting total RNA: 5 μg
% of mRNA in total RNA: 2%
Starting mRNA: (5 μg)*(0.02) = 0.1 μg
Average transcript length: 2,000 bases
Average MW of single base: 330 g/mole
Average MW of transcript: (2,000 bases)*((330 g/mole)/base) = 660,000 g/mole (660,000 g/mole)*(1 x 10^6 μg/g)*(1 mole/1 x 10^9 nmoles) = 660 μg/nmole (0.1 μg)*(1 nmole/660 μg) = 0.000152 nmole = 1.52 x 10-4 nmoles

Concentration in Terms of Complexity Ratio Calculation:
Complexity ratio, lys = (1.52 x 10^-9 nmoles)/(1.52 x 10^-4 nmoles) = 1 x 10^-5 1 x 10^-5 = 1/100,000

Answer Id: E14373

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Product FAQ

How long does the scan of a Mouse 430 2.0 Array take?

Answer

About 12 minutes per Mouse 430 2.0 Array, comparable to scan time for a set of Mouse 430A and Mouse 430B Arrays.

Answer Id: E13713

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