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Product FAQ

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 software, Edit > Set library path
c. Uninstall Expression Console. Download the Expression Console package from the 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: E14321

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Product FAQ

What is the mosaic call determination in ChAS?

Answer

The algorithm is designed to detect only mosaicism between ~30-70% for CNs between 1 and 3 for regions on the order of 5,000 markers in size or larger. The endpoint location of mosaic segments is less precise than the CN segmentation, with endpoint variation within 500 markers being typical for segments of 5,000 markers or larger. Some regions of full integer CN 1 or 3 below 5,000 markers in length may be incorrectly called as mosaic segments. Some regions of CN below 1 or above 3, mosaic or otherwise, less than 5,000 markers in length may be incorrectly called as mosaic segments.

Answer Id: E14006

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Product FAQ

What is the content of the SNP5.0 array?

Answer

The SNP 5.0 array contains all 500,568 SNPs from the original two chip Mapping 500K product. Using the current version of the algorithm (BRLMM), we are currently able to demonstrate that a set of 440,794 SNPs meet the specified performance criteria (see below). Advanced users can analyze the full set of 500,568 SNPs using an alternative library file (CDF) that reveals all the SNP content on the array. This advanced workflow can only be performed with the command-line “snp5-probeset-genotype” software.

In addition, there are 420.000 non-polymorphic probes, with great promise for copy number analysis.

Note: We have been collaborating with the Broad to develop the SNP 5.0 array, which combines the 500K SNPs on a single chip to decrease array processing time and improve ease of use. The single chip product was enabled by reducing the number of probes per SNP from 12 PM/MM (24 probes in total) to only 8 probes (2 PM with 4 replicates each).

Answer Id: E13738

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Product FAQ

How are custom CNV maps used with the copy number Segment Reporting Tool?

Answer

Users can generate custom CNV maps in the BED file format. The custom regions report will provide information on segments with copy number changes in the defined regions.

Answer Id: E13568

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Product FAQ

What is the difference between APT1 and APT2? How does that affect my data?

Answer

The higher-precision calculations algorithm in CHAS 3.1 and above might result in small numerical differences when compared to previous versions of ChAS. The changes in results are smaller than those seen in technical replicates run through the same version of ChAS. For further details, please contact techsupport@thermofisher.com

Answer Id: E13889

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Product FAQ

What are the major improvements in the design of the arrays in the GeneChip Rat Expression Set 230?

Answer

The Rat Expression Set 230 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 99, 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: E13804

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Product FAQ

What are the proper storage conditions for Thermo Fisher Scientific miRNA Arrays?

Answer

The arrays should be stored at 2-8 degrees C.

Answer Id: E14134

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Product FAQ

Does the protocol using the GeneChip Globin-Reduction Kit work with other Array systems?

Answer

The procedure has only been tested using the Affymetrix GeneChip system.

Answer Id: E13493

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Product FAQ

What is the reproducibility of GeneChip expression arrays?

Answer

GeneChip expression arrays generally have less than 2% false change. This result is determined by hybridizing a single sample to two arrays of the same type, and determining the percentage of probe sets that show a significant change. It has been shown that the false change rate from the arrays, as described previously, is significantly lower than the potential variabilities derived from different biological samples.

Answer Id: E13580

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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

Do we have to use any Affymetrix Reagents with our assay?

Answer

GeneChip Hybridization Control Kit 30 reactions
GeneTitan Hybridization, Wash, and Stain Kit for miRNA Array Plates 96 reactions
GeneTitan Hybridization Module for miRNA Plates 96 reactions
Affymetrix FlashTag Biotin HSR RNA Labeling Kit 10 reactions
Affymetrix FlashTag Biotin HSR RNA Labeling Kit 30 reactions

Answer Id: E14203

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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

Can I detect Insertions or Deletions on a resequencing array?

Answer

In general the arrays and software are most optimal for detection of SNPs. Unknown indels will be very difficult to automatically detect with the current array and software. For known indels we can try to tile (see below) for them but do not make any claims with respect to accuracy.
Indels: Known insertions can be tiled for.
Specific performance is not guaranteed.: Known homozygous deletions can be tiled for.
Specific performance is not guaranteed.: Unknown INDELS or heterogeneous deletions will not be detected.

Answer Id: E14173

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Product FAQ

For GeneChip experiments, can I measure the quality of a single hybridization without the rest of the experiment?

Answer

We does not recommend measuring the quality of a single-array performance without consideration for the rest of the experiment. In large-scale expression experiments using similar sample types, researchers are likely to develop their own single-array guidelines on what metric values are predictive of high- or poor-quality samples. However, these guidelines are likely to be dependent on sample type, and we are unable to recommend such guidelines for all possible situations. Note that the trend toward favoring model-based signal estimation algorithms (for all microarray experiments even beyond the Affymetrix platform) makes single-array quality determination very difficult due to the necessity of simultaneously analyzing multiple arrays to calculate signal estimates.

Answer Id: E14028

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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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