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Product FAQ

What Fluidics protocol do I use for the GeneChip Human Exon Array?

Answer

A new Fluidics Protocol has been developed for this assay, FS450_0001.

Answer Id: E13658

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Product FAQ

How many SNPs and Copy Number Probes are on the SNP 6.0 array?

Answer

906,600 SNPs on the SNP 6.0 array can be accessed utilizing Genotyping Console 2.1. In addition, the SNP 6.0 array contains 945,826 non-polymorphic “potential” copy number variation probes.

Answer Id: E13767

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Product FAQ

What is the basic principle of the ribosomal RNA reduction procedure using the RiboMinus Human/Mouse Transcriptome Isolation Kit?

Answer

Four biotinylated LNA RiboMinus probes are designed to specifically bind to the abundant 18S and 28S rRNA species (2 probes each for 18S and 28S rRNA). Following hybridization of the biotinylated probes to the rRNA molecules in the total RNA sample, the rRNA is efficiently removed from the sample by the addition of the RiboMinus Magnetic Beads that are coated with streptavidin. The unbound fraction represents the RNA with rRNA species reduced. The sample is then concentrated before target labeling using the IVT cRNA Cleanup Kit. Consult the handbook included in the RiboMinus Kit (https://tools.thermofisher.com/content/sfs/manuals/ribominus_human_mouse_man.pdf) for more details.

Answer Id: E13642

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Product FAQ

How is data security and backup implemented in Command Console Software?

Answer

Data security is controlled by the Windows folder, user, and group permissions. Also, chip rescans do not overwrite existing scan images. Data backup is achieved by standard methods for file backup, and data can easily be copied to external or network drives.

Answer Id: E14238

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Product FAQ

Can I perform the GeneChip Globin-Reduction kit protocol with less than 5 µg after concentration total RNA starting material?

Answer

The globin reduction method is optimized for use with 5 µg of total blood RNA. Starting with less than 5 µg is possible, but will lead to lower cRNA yields potentially leaving the user with insufficient material for hybridization.

Answer Id: E13487

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Product FAQ

What sample populations and criteria were used to select the markers for DMET Plus Array?

Answer

We used multiple populations (HapMap and Extended HapMap) when building the large internal reference set. The actual SNPs that are on the array come largely from the literature and we are unaware of any population bias that is in this collection. Much of the content did in fact come from the Pharma ADME web site. This consortia assembled a list of markers in genes that were prioritized into different classes. The most important of these is referred to as Core markers which mean that they have been validated in the scientific literature as having clinical relevance in drug responses. Markers were reviewed with several Pharmaceutical companies as well for input on important ADME markers.

Answer Id: E14292

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Product FAQ

Why do I have to incubate my PNA solutions before each use when using the GeneChip Globin-Reduction Kit?

Answer

In contrast to DNA oligonucleotides, PNA oligomers do not have a negatively charged backbone. Instead it is made from repeating N-(2-aminoethyl)-glycin units linked by peptide bonds. Additionally, they do not contain any pentose sugar moieties or phosphate groups. Because of these chemical characteristics, their water solubility is reduced in comparison to DNA oligonucleotides. To dissolve PNA molecules after storage below room temperature, the oligomers must first be incubated for 10 minutes at room temperature, then 10 minutes at 50 degrees C and then finally returned to room temperature before use.

Answer Id: E13497

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Product FAQ

Is the Command Console web server hosted by customers or by your company?

Answer

The Command Console web server is hosted by the customer.

Answer Id: E14220

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Product FAQ

What is the array format for the CytoScan HD Array?

Answer

CytoScan HD Array uses a 49 format and a 5-µm feature size.

Answer Id: E13988

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Product FAQ

Is it acceptable to make a master mix for the ELOSA QC hybridization solution (5X SSC, 0.05% SDS, 0.005% BSA and 25% dextran sulfate) to add to the 2 µL samples?

Answer

Yes.

Answer Id: E14076

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Product FAQ

What does the "_x_at" extension represent in the HG-U133 probe set name?

Answer

Occasionally, it is not possible to select either a unique probe set or a probe set with all probes common among multiple transcripts ("_s_at" ). In such cases, similarity criteria are suspended, and the resulting probe set name is appended with the "_x_at" extension. These probe sets contain some probes that are identical, or highly similar, to unrelated sequences. These probes may cross-hybridize in an unpredictable manner with sequences other than the main target. Data generated from these probe sets should be interpreted with caution, due to the likelihood that some of the signal is from transcripts other than the one being intentionally measured.

Answer Id: E14179

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Product FAQ

I need support assistance with an Affymetrix Power Tool (APT) related issue. What should I do?

Answer

Support for Affymetrix Power Tools (APT) is handled through the Affymetrix Developer Network. Questions, problems, feature requests and other issues can be addressed via techsupport@thermofisher.com. Because APT is not a commercial product, support for this is not available via commercial product support channels.

Answer Id: E14334

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Product FAQ

When using the ChAS software, is it important to back up my data?

Answer

Out of the six data files mentioned in the preceding question, it is important to back up and archive the ARR, CEL, CYCHP, and CHPCAR files at a minimum. This will allow you to maintain the ability to either reanalyze from the CEL file or re-visualize the results using the CYCHP/CHPCAR files

Answer Id: E13868

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Product FAQ

Can the Genome-Wide Human SNP Array 6.0 be used for copy number analysis?

Answer

Yes. The combination of the SNP Array 6.0 and Genotyping Console 2.1 provides a great set of tools for researchers who would like to study copy number changes in cancer as well as copy number variation in association studies.

Answer Id: E13749

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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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