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Product FAQ

In my sample, which RNA species are labeled with FlashTag reagent?

Answer

Any strand of RNA with a 3'OH will be labeled with FlashTag.

Answer Id: E14053

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Product FAQ

What are the 10 CytoScan assay processing steps listed in order?

Answer

The 10 assay processing steps, as listed in the CytoScan Assay User Manual (Cat. No. 703038) are the following:

1. Genomic DNA Preparation
2. NSP1 Restriction Enzyme Digestion
3. Ligation
4. PCR
5. PCR Product Purification
6. Quantitation
7. Fragmentation
8. Labeling
9. Hybridization
10. Wash, Stain, Scanning

Answer Id: E13962

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Product FAQ

What is the tolerance around hybridization time when working with Affymetrix miRNA Array strips?

Answer

We recommend maintaining consistency in array processing protocols to minimize introduction of variability. Our recommended hybridization time for Thermo Fisher Scientific miRNA Array Strip is 20 hrs.

Thermo Fisher Scientific miRNA Array Strip should be hybridized no less than 20 hrs and no longer than 24 hrs. We strongly encourage maintaining consistent hybridization times to avoid false positives with respect to differential expression due to hybridization time.

Answer Id: E14142

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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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Product FAQ

How is the CytoScan assay different from the assay used with Affymetrix Genome-Wide Human SNP Array 6.0?

Answer

The CytoScan assay has significantly fewer pipetting steps and requires less hands-on time than the Genome-Wide Human SNP 6.0 assay. The CytoScan assay uses only the Nsp I restriction enzyme and has been optimized for cytogenetics applications. The CytoScan assay is not intended for genome-wide association studies.

Answer Id: E13958

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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

How is fold change calculated in TAC?

Answer

Fold change is a number describing how much the signal changes from an initial condition group to a final condition group. These changes are represented in linear space. There are a couple of ways to describe fold change. One way a user might calculate this is to simply divide Sample A by Sample B and asses the result.

For example:
Array 1: Gene X - 1000 Gene Y - 5000 Gene Z - 500
Array 2: Gene X - 10000 Gene Y - 1000 Gene Z - 500
If comparing Array 1 vs Array 2: Gene X: 1000 / 10000 = 0.1 Gene Y: 5000 / 1000 = 5 Gene Z: 500 / 500 = 1
The way TAC displays fold change is to use the straight fold-change value if it is greater than or equal to 1.0 or display (-(1/fold change)) for values between 0 and 1. Let's look at the example above in TAC format:
Again, comparing Array 1 vs Array 2: Gene X: 1000 / 10000 = 0.1, so (-(1/0.1)) = -10 Gene Y: 5000 / 1000 = 5 Gene Z: 500 / 500 = 1
If doing the comparison the other way (Array 2 vs Array 1): Gene X: 10000 / 1000 = 10 Gene Y: 1000 / 5000 = 0.2 (or in TAC, (-(1/0.5)) = -5 Gene Z: 500 / 500 = 1

Answer Id: E14325

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Product FAQ

What is the difference between GeneChip miRNA 4.0 Cartridge Array, miRNA 4.1 Array Strip, and Affymetrix miRNA 4.1 Array Plate?

Answer

The arrays have the exact same design and contain the same number of probes and probe sets.

Answer Id: E14120

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Product FAQ

What are the product specifications of the SNP 5.0 array?

Answer

-QC call rate: 86%
-Minimum BRLMMP call rate: 97%
-Reproducibility: 99.9%
-Mendelian consistency: 99.9%
-Observed concordance with HapMap: >99.5%

Answer Id: E13742

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Product FAQ

How long does it take to scan an individual Affymetrix Mouse Diversity Genoytping Array?

Answer

Scanning an individual Mouse Diversity Genotyping Array takes about 35 mins.

Answer Id: E14156

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Product FAQ

How do I know if my first-cycle IVT reactions have worked well?

Answer

After the first cycle of amplification, it is often possible to quantitate the cRNA yield at this stage. Routinely, 400 ng - 1 µg of cRNA can be obtained from 50 to 100 ng of starting material. However, it is difficult to use the cRNA yield as the only metric to determine the success of the assay. Therefore, it may be most informative to combine the results from the first-cycle IVT yield with the second-cycle IVT yield, as well as array-quality metrics and data on various positive controls, to obtain a comprehensive view of how the assay has proceeded. [This answer refers to a product that has been discontinued.]

Answer Id: E14369

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Product FAQ

What analysis software packages are available for GeneChip Exon Array data analysis?

Answer

GeneChip Command Console (AGCC) is provided to control the fluidics station, 7G Scanner and generate .dat and .cel files. Probe level analysis of the .cel files is carried out by Expression Console. This software allows for the generation of signal estimates and detection p-values at the probe set level for either exon-level or gene-level analysis. Expression Console Software is freely downloadable from our web site and supported by the Technical Support team.

For additional higher levels of analysis, such as alternative splicing detection, a few experimental algorithms are published as methods in respective white papers. Users will need to implement these methods in advanced statistical analysis software packages. These methods have been developed based on experience with limited sample data sets, and further fine-tuning may be required depending on the user's unique biological systems. It is anticipated that new methods will continue to emerge to better support Exon Array analysis in the near future.

Answer Id: E13531

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Product FAQ

Under what conditions can TuScan estimate the percentage of aberrant cell fraction?

Answer

This is possible when:

The tumor is nearly homogeneous (i.e., it has a major dominant clone), and the percentage of aberrant cell fraction is 40% or higher.

Answer Id: E13860

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Product FAQ

How much does it cost to use the NetAffx Analysis Center?

Answer

The NetAffx Analysis Center is available to both customers and non-customers at no cost. The only requirement for use is the completion of a short registration form (http://www.affymetrix.com/analysis/index.affx#1_1).

Answer Id: E13457

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Product FAQ

What are the passing thresholds in GTC 4.2 for the Median Absolute Pairwise Difference (MAPD) metric?

Answer

The MAPD passing thresholds for SNP Array 6.0 copy number data are as follows:

-Affymetrix Reference: passing MAPD is 0.35 or less (Derived from the HapMap 270 data set)
-External Reference: passing MAPD is 0.35 or less (Chips generated in different lab and with different reagent lots)
-Internal Reference: passing MAPD is 0.30 or less (Chips generated in same lab with same reagent lots)

Answer Id: E13687

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