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Product FAQ

Should I treat my RNA sample with DNAse for FlashTag labeling?

Answer

DNAse treatment is optional. It is not necessary for RNA samples that have trace amounts of genomic DNA contamination, but it may be beneficial for RNA samples that are highly contaminated with genomic DNA, to more accurately quantitate the RNA. After treating your RNA with DNAse, it is essential that the DNase be inactivated completely before proceeding with the FlashTag procedure, to prevent degradation of the FlashTag reagent (Vial 5). A variety of RNA purification columns/kits may be used to inactivate the DNase. Inactivation of the DNase by high temperature may not completely inactivate the enzyme.

Answer Id: E14051

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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 arrays are supported for analysis on Genotyping Console Software (GTC)?

Answer

GTC is available to genotype the following arrays:
- Genome Wide SNP 5
- Genome Wide SNP 6
- Mapping 500K
- Mapping 100K
- Mouse Diversity array

Copy number and LOH analysis can be done on the:
- Genome Wide SNP 6
- Mapping 500K
- Mapping 100K

Answer Id: E14319

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Product FAQ

How are the probes for SNPs and Copy Number tiled on the SNP 6.0 array?

Answer

1. Each SNP is represented by a pair of 2 Perfect Match (PM) probe sequences, one for Allele A and one for Allele B, which are placed in adjacent positions on the array.
2. Each pair of SNP probes is replicated at least 3 times on the array. The replicates are distributed across the array such that each replicate is located in a different quadrant.
3. Copy-number probes are Perfect Match (PM) non-polymorphic sequences located in the stripes between quadrants.

Answer Id: E14296

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Product FAQ

Which format is the CytoScan XON array?

Answer

It is a 49 format array.

 

Answer Id: E16630

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Product FAQ

What is the total number of probes in OncoScan CNV Plus Assay Kit?

Answer

OncoScan CNV Plus Assay Kit has 217,454 probes.

Answer Id: E13849

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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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Product FAQ

How long does the scan of a HG-U133 Plus 2.0 Array take?

Answer

About 12 minutes per HG-U133 Plus 2.0 Array, comparable to scan time for a set of HG-U133A and HG-U133B Arrays.

Answer Id: E13783

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Product FAQ

What is the array format for the Genome-Wide Human SNP Array 6.0?

Answer

49 format, 5 µm Feature Size

All the SNPs are tiled with PM only 3-4 replicated probe pairs per SNP.

Answer Id: E13751

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Product FAQ

Can I run Affymetrix software on Windows XP?

Answer

All current Affymetrix software (Command Console, Genotyping Console, Expression Console, and Affymetrix Power Tools) are compatible with Windows XP.

Answer Id: E13526

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Product FAQ

What format is the Gene 2.0 ST Array?

Answer

The Gene 2.0 ST Array is a 100 format array.

Answer Id: E14100

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Product FAQ

How do the labels in the GeneChip IVT Labeling Kit work?

Answer

The IVT Labeling Kit contains a proprietary biotinylated nucleotide analog (patent pending). This analog is incorporated in the T7 RNA polymerase-mediated IVT amplification and labeling reaction as a pseudouridine reagent to generate cRNA targets.

Answer Id: E13612

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Product FAQ

What is the basic component in the DNA Labeling Reagent?

Answer

The key labeling molecule in the DNA Labeling Reagent is Biotin Allonamide Triphosphate.

Answer Id: E14191

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Product FAQ

Will new scripts need to be uploaded in GCAS for the new plate?

Answer

No, new scripts for Hyb, Wash, and Stain of the HT HMR PM only array plates will not be needed. The script is the same as the old HMR plate arrays.

Answer Id: E13600

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Product FAQ

What copy number calls do I get from TuScan?

Answer

Log2 and B-allele frequency.

Linear copy number calls when you mouse over aberrations. In some cases, linear calls are calls in aberrant cell fraction only. In the software, when the percentage of aberrant cells has a percentage value, the linear call for aberrations in that sample is the call in the aberrant cells only. Values will be integers. When the percentage of aberrant cells is “N/A,” the linear call is an average call across the aberrant and non-aberrant cells, and values will be non-integers. You can estimate the copy number in aberrant cells if you have an independent tumor burden estimate.

Answer Id: E13858

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