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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 are the general genomic DNA requirements for the CytoScan assay?

Answer

DNA must be double-stranded genomic DNA.
DNA must be free of PCR inhibitors.
DNA must not be contaminated with other human genomic DNA sources or with genomic DNA from other organisms.
DNA must not be degraded.
DNA should have an A260/A280 between 1.7-2.1 (numeric rounding allowed).

Answer Id: E13949

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Product FAQ

What is the recommended genomic DNA extraction methods used for the CytoScan assay?

Answer

Both blood and cell line sample sources have been tested with the CytoScan assay.
Methods that include boiling or strong denaturants are not acceptable because the DNA would be rendered single-stranded. Genomic DNA extracted using the following methods have been tested at ThermoFisher Scientific:

QIAGEN - Gentra Puregene Kit
5 PRIME - PerfectPure DNA Blood Kit
The CytoScan assay requires genomic DNA concentration >50 ng/µL. Therefore, the elution volumes for each of the kits will need to be adjusted accordingly to achieve the desired concentration.

Answer Id: E13950

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Product FAQ

Which Affymetrix platforms support CNP analysis?

Answer

CNP analysis is supported in GTC 4.2 for the SNP Array 6.0.

Answer Id: E13696

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Product FAQ

How many freeze/thaw cycles are validated for CytoScan Reagent Kit (24 samples)?

Answer

CytoScan Reagent Kit (Cat. No. 901808) is validated for for 4 in-use freeze/thaw events but have to use the kit within a month (30 days) once opened even if they have not gone through 4 freeze-thaws.

Answer Id: E13951

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Product FAQ

How many samples should be processed at a time using the CytoScan assay?

Answer

It is recommended to run no more than 24 samples at a time. The assay is a four-day protocol; however, the technician can use an optional three-day protocol after becoming comfortable with the assay.

Answer Id: E13952

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Product FAQ

What should I do if I see a smear in their negative control on their PCR gel when performing the CytoScan assay?

Answer

A smear in the negative control indicates there has been a contamination. If the negative control band is a light smear, it could be a low-level environmental bacterial contaminant introduced through plastic surfaces. This has shown not to have a material impact on the CytoScan HD data. If a bright band or a smaller smear is seen, then that could be a real cross-contaminant from a sample, and the samples would need to be checked for contamination. If a smear is seen in the negative control well, you should re-run the negative control to verify this was not a result of sample bleed-over from gel loading.

Answer Id: E13969

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Product FAQ

Is there a genetic map and other SNP annotations with the Mapping arrays?

Answer

Yes, there is a variety of SNP annotations that are available through the NetAffx Analysis Center, including deCode and Marshfield genetic maps, allele frequency in three populations, chromosome, physical position, cytoband, and nearest genes.

Answer Id: E13703

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Product FAQ

How many SNP and CN probes are included on CytoScan Optima Array?

Answer

CytoScan Optima Array has a total of 315,608 features covering control, CN, and SNP probes. There are a total of 18,018 non polymorphic CN probes and 148,450 SNP markers on the Optima Suite.

Answer Id: E13840

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Product FAQ

What thermal cycler can be used for the CytoScan Assay?

Answer

The ABI 9700 (silver or gold-plated silver block only; do not use an aluminum block) and the ABI 2720 (pre-PCR room only) thermal cyclers have been validated for the CytoScan Assay.

Answer Id: E13898

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Product FAQ

What are the fill volumes of the reagents in CytoScan Reagent Kit?

Answer

Only the volume that is indicated on the label can be guaranteed. Since our assurance guarantee is only provided for the label volume, it is advised not to plan experiments or standard operating procedures based on potential overage volumes.

Answer Id: E13953

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Product FAQ

What are the major improvements in the design of the arrays in the GeneChip Mouse Expression Set 430?

Answer

The Mouse Expression Set 430 incorporates the same expertise that was utilized for the design and performance of the GeneChip Human Genome U133 Set. For the design, genomic sequences were used to verify sequence selection, orientation, and the quality of sequence clustering. Additionally, clustering information from UniGene, build 107, was used with primary sequences and annotation information combined from a large variety of public databases to provide a more complete and accurate starting sequence data set.

Answer Id: E13720

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Product FAQ

When should 500K enzymes be vortexed?

Answer

The enzyme alone should never be vortexed. The final cocktail, when specified, can be vortexed.

Answer Id: E13704

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Product FAQ

Which assay do you recommend for use with Affymetrix GeneChip miRNA Arrays?

Answer

Affymetrix only supports use of the Affymetrix FlashTag Biotin HSR RNA Labeling Kit for preparing targets to be applied to GeneChip miRNA Array, Affymetrix miRNA Array Strip, and Affymetrix miRNA Array Plate. This product may be ordered through Affymetrix using Cat. No.s 901910 for the 10- reaction kit and 901911 for the 30-reaction kit.

Answer Id: E14124

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Product FAQ

How can the Mismatch probe cell have a higher intensity than its complementary Perfect Match probe cell?

Answer

There can be a number of reasons for this. It is possible that the probe sequence has high homology with another unknown sequence, resulting in a high Mismatch-to-Perfect Match ratio. Another possibility is that the probe sequence on the array is correct for the majority of the cases, however, the sample may have a sequence variation that causes low specific binding to the Perfect Match, and high specific binding to the Mismatch.

Regardless of the cause, the redundancy of the number of probes representing a sequence on GeneChip expression arrays negates any significant impact this may have on the final interpretation of the data.

Answer Id: E13520

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