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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

Error when exporting in VCF format in Axiom Analysis Suite, there is no genotyping information in the exported file. Instead of genotypes there is only "./." for all samples on all SNPs. What should I do?

Answer

In order to export in VCF format from the Axiom Analysis Suite, the annotation files need to have the ref and alt allele columns. If these columns are blank in the annotations, the software will export "./." in place of genotypes.

Answer Id: E14330

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Product FAQ

Can the Affymetrix Mouse Diversity Genoytping Array be used for copy number analysis?

Answer

Yes. The array contains more than 916,000 non-polymorphic copy number probe sets for the detection of copy number variation-the largest number of copy number probes for mice on the market. These probe sets are targeted to functional elements and regions known to harbor segmental duplications.

However, because so little information on copy number variation in mice exists, the copy number application is for discovery use only. Copy number analysis is not supported because there are no known informatics tools for this purpose. You can find annotation comma-separated values (CSV) files for the copy number probes by visiting the NetAffx Analysis Center and selecting the Mouse Diversity Array.

Answer Id: E14148

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Product FAQ

The Expression Console Software displays an error when trying to download library files for the first time after installation of the software. What should I do?

Answer

a. Check Operating System of computer and make sure compatible with the Expression Console version installing.
b. Check to make sure the library path for Expression Console is local and not under “My Documents”. In Expression Console, Edit > Set library path
c. Uninstall Expression Console. Download the Expression Console package from our website. Unpackage the download. Right mouse click on the setup.exe file and “run as administrator”. Make sure the library path is local.

Answer Id: E14331

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Product FAQ

Where can I find annotation and information regarding the probes for the Affymetrix Mouse Diversity Genoytping Array?

Answer

Please visit the website of The Jackson Laboratory, which has annotation for all the probes. These annotation files will be updated regularly. You can also find the annotation files for SNP and copy number probes by visiting the NetAffx Analysis Center and choosing “Mouse Diversity Array” from the drop-down menu. Sample data, probe set data, library files, alignment, annotation, and sequence files can be found at www.thermofisher.com.

Answer Id: E14149

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Product FAQ

Do I have to normalize my samples prior to starting this new 3' IVT Express Kit?

Answer

Yes, we have seen slight differences in the data when starting with 50ng vs. 500ng of the same total RNA. We would recommend normalizing the starting material so all samples have the same amount of RNA prior to starting the protocol. [This answer refers to a product that has been discontinued.]

Answer Id: E14351

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Product FAQ

How do I limit an analysis in the TAC software to my genes of interest?

Answer

In the TAC software, you can filter the list of results by a list of gene symbols. This will also limit the hierarchical clustering of your expression data to the gene symbols found on your list. To do this, proceed with your analysis as you normally would. Once the results are returned, in the Table tab, you right click on the Gene Symbol column and choose the Filter option. A pop up will then appear allowing you to apply the filter logic. To filter on a list of Gene Symbols, select either the ‘In List’ or ‘Not In List’ option, as it pertains to your query. The Edit List window will appear, allowing you to type or paste in gene symbols. These must be separated by comma, semi-colon, or line breaks to be recognized properly by the software. Please also note that we use the official gene symbol determined by the NCBI Gene database. If your gene symbol of interest does not appear to function properly, please confirm that it is the official gene symbol by consulting the NCBI Gene database website.

Answer Id: E14332

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Product FAQ

What performance can I expect from studies involving wild-derived strains for the Affymetrix Mouse Diversity Genoytping Array?

Answer

We have performance metrics for using the Mouse Diversity Genotyping Array with classic inbred laboratory strains and F1 crosses between these inbred strains, but we do not currently offer comprehensive metrics for wild-derived strains.

Table 2 of the supplement to the publication “A customized and versatile high-density genotyping array for the mouse” (Yang H., et al., Nature Methods, 2009), shows performance (call, heterozygosity, and concordance rates) of the array for six wild-derived strains: WSB/EiJ, PWD/EiJ, MOLF/EiJ, CAST/EiJ, SPRET/EiJ, and PANCEVO/EiJ, representing M. m. domesticus, M. M. musculus, M. m. castaneus, M. m. molosinnus subspecies, and M. spretus and M. spicilegus species, respectively. The array performance was highest for wild-derived strains from M. m. domesticus subspecies, followed by strains from other Mus subspecies, which reflects the degree of genetic divergence from the reference strain used C57BL/6J.

The least divergent strain, WSB/EiJ, had the highest call and concordance rates (98.041, 0.992) and lowest heterozygosity rate (2.445), while the most divergent strain, SPRET/EiJ, had the lowest call and concordance rates (92.386, 0.986) and highest heterozygosity rate (14.797).

Answer Id: E14150

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Product FAQ

For Thermo Fisher Scientific microarrays, what does high background mean?

Answer

A high background implies that impurities, such as cell debris and salts, are binding to the probe array in a nonspecific manner and that these substances are fluorescing at 570 nm (the scanning wavelength). This nonspecific binding causes a low signal to noise ratio (SNR), meaning that genes for transcripts present at very low levels in the sample may incorrectly be called Absent. High background creates an overall loss of sensitivity in the experiment.

Answer Id: E13522

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Product FAQ

I notice the cDNA clean up step has been removed from this protocol. Can I also leave the cDNA clean up step out of the One-Cycle Kit?

Answer

We have not validated removal of the cDNA clean up step in the One-Cycle protocol. [This answer refers to a product that has been discontinued.]

Answer Id: E14352

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Product FAQ

I am getting an error warning message upon launch of AGCC Portal: “Caution: The browser you are using is not a recommended browser for AGCC. Recommended browsers are: Microsoft Internet Explorer 7.0 or newer Mozilla Firefox 2.0 or newer”. What should I do?

Answer

Even though the browser being used is above IE version 7 this warning message can appear. To remove the message (Reference from AGCC 4.1.2 Release Notes) "If you log into the system and open the web portal under multiple user accounts, you may see a warning message indicating that Internet Explorer 11 is not a recommended browser. This message can be cleared by adding the localhost website (the AGCC web portal) to the compatibility view list, by opening the Tools menu (click gear icon at upper right corner, or type ALT-X), click Compatibility View Settings, and then adding localhost to the list using the 'add' button."

Answer Id: E14333

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Product FAQ

If I suspect my gDNA requires further purification when using an Axiom array, what is the recommended cleanup protocol?

Answer

If gDNA preparation is suspected to contain inhibitors, the following cleanup procedure can be used:
1. Add 0.5 volumes of 7.5 M NH4OAc, 2.5 volumes of absolute ethanol (stored at -20 degrees C), to gDNA.
2. Vortex and incubate at -20 degrees C for 1 hr.
3. Centrifuge at 12,000 x g in a microcentrifuge at room temperature for 20 min.
4. Remove supernatant and wash pellet with 80% ethanol.
5. Centrifuge at 12,000 x g at room temperature for 5 min.
6. Remove the 80% ethanol and repeat the 80% ethanol wash one more time.
7. Resuspend the pellet in reduced EDTA TE Buffer (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA).

Answer Id: E14286

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Product FAQ

Where can I obtain sequence information for the probes and probe sets represented on the arrays in the GeneChip Mouse Expression Set 430?

Answer

Complete sequence information for the probes, target, and consensus/exemplar sequences represented on all catalog expression arrays, including the Mouse 430, are available through the Support by Product page.

Answer Id: E13725

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Product FAQ

Can I obtain sequence information for the probes represented on the arrays in the HG-U133 Set

Answer

Yes, the complete set of sequence information for the probes, target, and consensus/exemplar sequences represented on all catalog expression arrays, including the HG-U133 Set, is available. Please check the HG-U133 techncial note (https://tools.thermofisher.com/content/sfs/brochures/hgu133_design_technote.pdf).

Answer Id: E13774

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Product FAQ

Why is my accession number missing from the Thermo Fisher Scientific sub-cluster?

Answer

For any particular array set, there are probe sets for only a subset of all possible sub-clusters. Moreover, some sequences are excluded because they are of low quality or are problematic (for example, too short or too repetitive), while other sequences have been added to the public databases since the array was designed. If you cannot find your sequence identifier, try running BLAST to search for a similar sequence or using the Probe Match tool (https://tools.thermofisher.com/content/sfs/manuals/probematch_manual.pdf).

Please note: You have to search all the sub-clusters from a UniGene cluster before concluding that your sequence is missing in the sub-cluster databank.

Answer Id: E13473

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