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Product FAQ

Can I get gene-level expression results for GeneChip Exon arrays?

Answer

The current exon array analysis software allows for the aggregation of multiple exon level probe sets into a larger "meta probe set". PLIER signal estimates and DABG detection values are then computed for these meta probe sets. The definition and grouping of the exons into a gene can have a significant impact on the final signal value of a particular gene. Affymetrix recommends using the "core gene" grouping or the "full gene" grouping files to derive the gene-level signal that should most resemble the expression of the constitutive exons.

See the "Gene Signal Estimates from Exon Arrays" (https://tools.thermofisher.com/content/sfs/brochures/exon_gene_signal_estimate_whitepaper.pdf) white paper for more information.

Answer Id: E13535

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Product FAQ

For the CytoScan assay, is there a plate purification option for the PCR product purification step?

Answer

No, only the single-tube purification process is validated with the assay.

Answer Id: E13970

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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

How are DAT and CEL data files analyzed?

Answer

DAT and CEL data are analyzed in the Command Console Viewer. By default, Command Console Software automatically grids the DAT file and creates the CEL data. Please see demo in the training and tutorials section of the website (www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-analysis-learning-center/microarray-analysis-training.html).

Answer Id: E14247

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Product FAQ

What are the available assay options for running the Clariom S array?

Answer

Depending on input, sample type, and platform, you have several options:
Cartridge: Assays for 100 pg-50 ng of total RNA isolated from whole blood, cultured cells, and fresh/fresh frozen or FFPE tissues.
Pico Assay Assays for 50-500 ng of total RNA isolated from whole blood, cultured cells, and fresh/fresh frozen tissues.
WT Plus Assay Plates: Assays for 100 pg-50 ng of total RNA isolated from whole blood, cultured cells, and fresh/fresh frozen or FFPE tissues for analysis on GeneTitan Instrument.
Pico Assay HT Assays for 50-500 ng of total RNA isolated from whole blood, cultured cells, and fresh/fresh frozen tissues for analysis on GeneTitan Instrument.

Answer Id: E14312

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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 are the safe stopping points in the GeneChip expression assay?

Answer

It is safe to stop work after each of the major steps in the sample preparation process: first-strand cDNA synthesis, second-strand cDNA synthesis, IVT, labeling, and after mixing the hybridization cocktail. If possible, work with extracted RNA samples immediately, rather than freezing them although it is common practice to use stored, frozen RNA samples in the process.

Answer Id: E13590

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Product FAQ

In the Command Console Software, what are templates?

Answer

Templates are used to store groups of attributes and their controlled vocabularies. Controlled vocabularies can be used to enforce consistent metadata within studies.

Answer Id: E14237

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Product FAQ

Can I combine the CEL files from GeneChip miRNA 3.0 Cartridge Arrays, Affymetrix miRNA 3.1 Array Strips, and Affymetrix miRNA 3.1 Array Plates into the same experiment?

Answer

No, the CEL files from GeneChip miRNA 3.0 Cartridge Array, Affymetrix miRNA 3.1 Array Strip, and Affymetrix miRNA 3.1 Array Plates are not compatible.

Answer Id: E14121

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Product FAQ

Which fluidics script should I use for the SNP 6.0 array?

Answer

Genome-Wide Human SNP Array 6.0, Fluidic Scripts for FS450 is GenomeWideSNP6_450, Library Files named GenomeWideSNP_6

Answer Id: E13766

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Product FAQ

Does this method of globin-reduction work with RNA isolated from fetal blood when using the GeneChip Globin-Reduction kit?

Answer

No. The PNA oligo sequences are specific to the alpha and beta globin genes that are predominantly expressed in adult reticulocytes. In fetal blood, fetal globin is preferentially expressed instead. There is sufficient sequence divergence between the adult and fetal genes that the current PNA oligomer sequences are not expected to hybridize to fetal globin mRNA.

Answer Id: E13480

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Product FAQ

What file sizes are associated with CytoScan Optima Array?

Answer

The CEL file is ~3 MB, and the CYCHP file is ~18 MB

Answer Id: E13841

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Product FAQ

Why is only 2 µg of RNA used for the control reactions in the GenChip Globin-Reduction kit?

Answer

The RNA controls are designed to mimic a common human blood RNA sample. That means the amount of globin in vitro transcripts included in the Jurkat + Globin RNA control is adjusted to result in signal intensities for alpha globin and beta globin similar to a typical blood RNA sample when starting with 5 µg of material. These controls demonstrate the effect of excess globin mRNA transcripts typically observed in human whole blood samples on GeneChip expression analysis results and are used to verify the effectiveness and specificity of the globin reduction process. 2 µg of control RNA is sufficient to assess these key points.

Answer Id: E13489

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Product FAQ

The FlashTag HSR Range of Sensitivity is described in amoles; how does that translate to copies of microRNA?

Answer

The dynamic range of detection on a per molecule basis for any given miRNA is:

0.5 amoles = 300,000 copies
7400 amoles = 4,440,000,000 copies

Answer Id: E14058

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Product FAQ

What is the GeneChip Command Console Software?

Answer

The GeneChip Command Console Software is the next generation of Affymetrix core software and replaces the GCOS software suite. Command Console Software provides instrument control, sample registration, and data management capabilities. It supports the microarray workflow from sample registration through CEL file generation.

Answer Id: E14210

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