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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 median of the absolute values of all pairwise differences (MAPD), and how should it be used?

Answer

MAPD is a per-microarray estimate of variability, like standard deviation (SD) or interquartile range (IQR). It measures the variability in log2 ratios by looking at the pair difference of all probes and taking a median value. The effect of an occasional big difference in log2 ratios between probes is removed by taking a median value and not a mean. This variability can come from different sources:

-Intrinsic variability in the starting material, hybridization cocktail preparation, microarray, or scanner
-Apparent variability induced by the fact that the reference may have systematic differences from the sample on this microarray

Regardless of the source of variability, increased variability decreases the quality of the CN calls. A high MAPD can be attributed to any of the above factors and indicates that CN calls may be inaccurate, leading to a higher false positive/negative rate.

Answer Id: E13842

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Product FAQ

Does this Two-Cycle cDNA Synthesis Kit/protocol work well on partially degraded RNA samples?

Answer

No. Similar to previous recommendations for the standard protocol and SSTLvII, the Two-Cycle cDNA Synthesis Kit protocol also requires high-quality total RNA as starting material. Most commonly, customers assess OD260/280 ratios together with electrophoretic analysis results when sufficient material is available. When sample quantity is limiting, the combination of RiboGreen for quantitation and Bioanalyzer for quality assessment has worked quite well. To better distinguish whether the starting material quality has affected the target labeling process, it is recommended to use the GeneChip Eukaryotic Poly-A RNA Control Kit and spike the positive controls into the starting materials for efficient troubleshooting. [This answer refers to a product that has been discontinued.]

Answer Id: E14363

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Product FAQ

What is SNP quality control (SNPQC), and how should it be used?

Answer

SNPQC is a measure of how well genotype alleles are resolved in the microarray data. In other words, it estimates the distributions of homozygous AA, heterozygous AB, and homozygous BB alleles and calculates the distance between them. The better the separation of these distributions, the better the ability to identify a genotype based on its cluster position. A low SNPQC value indicates that the quality of the SNP allele data is compromised due to higher noise within the array, which compromises the overall quality and clarity of results.

Answer Id: E13843

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Product FAQ

How does your Two-Cycle cDNA Synthesis Kit protocol perform compared with Ambion's MessageAmp Kit or Arcturus's RiboAmp Kit?

Answer

GeneChip assays are an integrated part of the complete system solution and are the only reagent kits developed and fully validated on GeneChip brand arrays. With a thorough understanding of the performance characteristics of the GeneChip reagent kits on GeneChip arrays, users should have more confidence in obtaining meaningful results. Affymetrix has been very diligent in investigating alternative target labeling protocols to ensure that researchers have access to the most robust and standardized assays when running GeneChip arrays. Affymetrix believes that the current set of GeneChip reagents are the most optimized solutions and can help customers extract the most reproducible and reliable data on GeneChip arrays. Affymetrix will continue to research alternative procedures to evolve the assay for improved ease of use and more streamlined assays. [This answer refers to a product that has been discontinued.]

Answer Id: E14364

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Product FAQ

In a hypothetical CytoScan assay failure in which PCR fragment size distribution observed on the PCR gel is significantly greater than 2,000 bp DNA smear, what processes in the assay could play a role in the failure?

Answer

The digestion step could be root cause. If the reaction did not go to completion, there may be, on average, longer fragments at the end of the reaction. These longer fragments then pass on to ligation and PCR reactions.

Insufficient amounts of PCR primer were added to facilitate suppression PCR. The primer concentration shifts the PCR reaction equilibrium toward larger fragment distributions, in this case, by increasingly unfolding (linearizing) the stem-loop structure at increasing primer concentration when the same adaptor ends hybridize.

Answer Id: E13967

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Product FAQ

What is waviness standard deviation (Waviness-SD), and how should it be used?

Answer

Waviness-SD is a global measure of variation of microarray probes that is insensitive to short-range variation and focuses on long-range variation. Based on an empirical testing dataset, we have determined that array data with Waviness-SD >0.12 has either sample or processing batch effects that will reduce the quality of the copy number calls. Elevated Waviness-SD is not always an indication of too much noise. Elevated waviness with good MAPD and SNPQC metrics can occur in samples with many copy number changes. Therefore, it is advised to check the data when observing elevated waviness with good MAPD and SNPQC. The Waviness-SD metric is applicable to constitutional blood and cell line data. The Waviness-SD metric is not intended for alternative sample types such as cancer samples in which the results may vary as a result of the biological complexity. For these sample types, it is recommended to use the ndwavinessSD.

Answer Id: E13844

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Product FAQ

Can you provide more information about the 420.000 non polymorphic probes and their application?

Answer

100K probes were picked to cover 2000 germline copy number variants (CNV) identified in the UCSC database with 50 probes each. The other 320,000 were picked to give even spacing across the genome, concentrating on areas that do not already have SNP coverage.

Answer Id: E13739

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Product FAQ

What is the detection sensitivity of the Two-Cycle cDNA Synthesis Kit protocol?

Answer

One way to assess the assay sensitivity is to monitor the global array metric of percent Present calls. From the same high-quality starting material, the Two-Cycle cDNA Synthesis protocol demonstrates highly comparable P% calls as the results generated from the One-Cycle cDNA Synthesis protocol. Another way to estimate the detection sensitivity is to use poly-A RNA spike-in controls. Following the recommended protocol included in the GeneChip Eukaryotic Poly-A RNA Control Kit, the Two-Cycle cDNA Synthesis Kit generally amplifies the samples sufficiently to detect the 3'-Probe Set of lys (the transcript with the lowest concentration, at 1:100,000 complexity ratio) as Present over 70% of the time. [This answer refers to a product that has been discontinued.]

Answer Id: E14365

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Product FAQ

What format are the human, mouse, or rat transcriptome arrays?

Answer

Human, mouse, or rat transcriptome arrays are 49-format.

Answer Id: E14106

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Product FAQ

What was the criteria for selecting covered species on the Axiom Microbiome Array?

Answer

The species included on the array represent all known microbial sequences available in the NCBI database as of October 2014 for which probes could be designed. Any sequences deposited after October 2014 are not represented on the array.

Answer Id: E14301

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Product FAQ

Do users have to copy the sample/array attribute file with CEL data to other systems?

Answer

This is optional. Please see the previous question regarding the benefits of sample/array registration and the training and tutorials (www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-analysis-learning-center/microarray-analysis-training.html) section of the website on how to run arrays through fluidics and scanning on different computer workstations.

Answer Id: E14257

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Product FAQ

For the CytoScan assay, does the PCR have to be set up in a separate pre-PCR clean room?

Answer

Using two separate rooms greatly reduces the risk of sample contamination by previously amplified PCR products. If only one room is available, designate one area of the room as the pre-PCR clean area and a separate area as the post-PCR clean area. If a one-room configuration is being used, it is highly recommended to use a laminar flow cabinet for the pre-PCR clean area. See the CytoScan Assay User Manual (Cat. No. 703038, https://tools.thermofisher.com/content/sfs/manuals/cytoscan_assay_user_manual.pdf) for more details about the recommended laboratory setup.

Answer Id: E13968

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Product FAQ

Which GCOS features are not supported in Command Console Software?

Answer

Publishing and publish databases will not be supported. However, customers can leverage the flexibility of the file-based system to populate their own library information management systems (LIMS).
CHP data will be generated by separate Affymetrix and third-party applications, including Expression Console Software and Genotyping Console Software.
GeneArray 2500 and Fluidics Station FS400 instruments are not supported by Command Console Software.
Windows 2000 operating system is not supported.

Answer Id: E14228

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Product FAQ

How long can for the CytoScan 750K Arrays be stored in holding buffer before scanning?

Answer

After the washing and staining step, arrays can be stored for up to 24 hours at 40 degrees C before scanning.

Answer Id: E13923

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