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Product FAQ

What are the GeneChip™ Operating Software (GCOS) and GCOS Server Software (GCOS Server) products?

Answer

The GeneChip™ Operating Software (GCOS) is an operating system software that controls our instruments, acquires data, and executes gene expression analysis. In addition, GCOS contains an embedded database that manages both experiment information and data. Stratagene™ Array Assist Lite, Affymetrix™ GeneChip™ Sequence Analysis Software (GSEQ), Affymetrix™ GeneChip™ Genotyping Analysis Software (GTYPE), Affymetrix™ GeneChip™ Targeted Genotyping Analysis Software (GTGS) use data from the GCOS Database for gene expression cluster/statistical analysis, sequencing analysis and genotyping data analysis, respectively.

GCOS desktop version (client) can be conveniently upgraded to GCOS Server. With GCOS Server, customers benefit from increased systems flexibility, streamlined user interface integration, enhanced automation, and robust data handling and security. Using either an Oracle or SQL based server, researchers can perform a variety of data management tasks and data queries. Plus, extensive security features are available to allow users secure access to their data.

Answer Id: E13556

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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

My genomic DNA sample for the Axiom™ array is showing RNA contamination, what can I do?

Answer

The biggest risk is underestimation of the amount of input gDNA. You should quantify by PicoGreen™ assay to ensure you are adding the correct amount of starting DNA into the reaction. The contaminating RNA should not affect the assay. If a PicoGreen™ assay is not an option, you may need to clean up the sample to get a better assessment of the actual amount and quality of gDNA.

Answer Id: E14287

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Product FAQ

When using the ChAS 3.1 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

Why should I choose the Genome-Wide Human SNP Array 6.0 array platform for copy number analysis?

Answer

The SNP Array 6.0 provides:

-The highest resolution across the genome to detect and define chromosomal aberrations.

-The average median SNP + CNV inter-marker distance is 680 base pairs. It also has the highest coverage of known copy number variants (90.5% of 3400 known regions). This gives researchers more power and confidence to detect chromosomal aberrations and makes it easier to define boundaries and breakpoints.

-Provides allele-specific copy number. This allows customers to perform LOH and allele-specific analyses. The clear advantage of including this information is in the ability to differentiate between mechanisms which cause the underlying biological effect. For example, a copy-neutral event is only detectable with this additional information. A copy neutral event is detected as no change in copy number but LOH is present.

-A platform that supports a portfolio of products for genomic research-copy number genotype, gene expression and splice variant analysis on a single industry standard microarray platform.

Answer Id: E13750

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Product FAQ

What is the required input for the Axiom™ Microbiome Array?

Answer

50 ng of input mass is optimal.

Answer Id: E14288

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Product FAQ

What is the recommended operating system for ChAS 3.1?

Answer

A 64-bit system is required to generate and view CytoScan™ CYCHP data files. The recommended system requirements are Windows™ 7 Professional SP1 and Windows™ 8.1. ChAS 3.1 requires Affymetrix’ GeneChip™ Command Console™ Software (AGCC) 3.2.4 or higher to produce CytoScan™ CEL files. For more details on the system and hardware requirements, please refer to ChAS 3.1 User Guide or the minimum software and hardware requirements documents on our web page

Answer Id: E13869

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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

Will I be able to use %P to assess the quality of my scans?

Answer

No, %P is a metric derived using the MAS5 algorithm which has been disabled for the HT PM Plate Arrays.

Answer Id: E13601

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Product FAQ

What are the definitions of the array QC metrics terms "MAPD" and "SNPQC"; what does each metric measure and how are they used in assessing array performance?

Answer

MAPD: Median of the Absolute values of all Pairwise Differences is a per-microarray estimate of variability, like standard deviation (SD) or interquartile range (IQR). It measures the variability in log2 ratios by looking at the pair difference of all probes and taking a median value. The effect of an occasional big difference in log2 ratios between probes is removed by taking a median value and not a mean. This variability can come from different sources: Intrinsic variability in the starting material, hybridization cocktail preparation, microarray, or scanner.

Apparent variability induced by the fact that the reference may have systematic differences from the sample on this microarray. Regardless of the source of variability, increased variability decreases the quality of the CN calls. A high MAPD can be attributed to any of the above factors and indicates that CN calls may be inaccurate, leading to a higher false positive/negative rate.

SNPQC: This is a measure of how well genotype alleles are resolved in the microarray data. In other words, it estimates the distributions of homozygous AA, heterozygous AB, and homozygous BB alleles and calculates the distance between them. The better the separation of these distributions, the better the ability to identify a genotype based on its cluster position. The larger the difference between the peaks and the troughs, the better the resolution of homozygotes and heterozygotes and the higher the SNPQC metric is. If the three peaks are not well resolved, the difference between peaks and troughs will be low, resulting in a lower SNPQC value. A low SNPQC value indicates that quality of the SNP allele data is compromised, due to higher noise within the array, which compromises the overall quality and clarity of results.

Answer Id: E13996

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Product FAQ

How do I use the new .ps files for limiting the data output to human, mouse, or rat probe sets in Expression Console Software?

Answer

To use the new .ps files, you must download the Affymetrix™ miRNA 3.1 library analysis file package (miRNA-3_0-st-v3_analysis.library_files.20121130, or newer) from the product or support web page and place all files in the folder used for Expression Console analysis library files. Restart Expression Console Software (if open) and reload the existing study, or create a new study. When you click the “Run Analysis” button, a pop-up window will appear and provide you with a listing of available analyses. These include:
1) All probe sets for all organisms
2) Human only probe sets
3) Mouse only probe sets
4) Rat only probe sets.

All 4 of these analysis options include the choice of RMA+DABG with and without normalization.

Answer Id: E14202

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Product FAQ

What is the PhyloChip Array and can I run it in my lab?

Answer

The PhyloChip Array is a custom array currently developed by Dr. Gary Andersen at the Lawrence Berkeley National Laboratory. The array identifies and measures the relative abundance of greater than 50,000 individual microbes. PhyloChip relies on the analysis of all nine variable regions of the 16S gene, providing more in-depth taxonomic classification than other common approaches. The array is only available through Second Genome Solutions and cannot be purchased directly from our company.

Answer Id: E14306

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Product FAQ

What is the genomic DNA input amount required for the SNP 6.0 Assay?

Answer

The SNP 6.0 Assay requires 500 ng genomic DNA.

Answer Id: E14289

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Product FAQ

What is the content of the Genome-Wide Human SNP Array 6.0?

Answer

-Contains 906,600 SNPs
-Contains 946,000 Non-Polymorphic Probes
-All screened in 500 distinct samples (270 HapMap plus diversity panels)
-Unbiased selection of 494,000 SNPs from 5.0 and 500k tiled on the 6.0
-6k SNPs not tiled due to lack of cluster classification or multiple hits to the genome.
-482,000 SNPs; historical SNPs from 500k and 5.0 out of the 494,000 SNPs can be analyzed with the default library file and the SNP 6.0 genotyping algorithm (Birdseed)
-Selection of additional 424,000 SNPs
-Tag SNPs
-SNPs from chromosomes X
-Y Chromosome SNPs (257 in default, 900 in full)
-Y Chromosome CN Probes (8,583)
-Mitochondrial SNPs (119 in default, 465 in full)
-100K New SNPs added to the HapMap database
-SNPs in recombination hotspots

Answer Id: E13752

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Product FAQ

How many single nucleotide polymorphism (SNP) and copy number (CN) probes are included on the CytoScan™ HD Array?

Answer

CytoScan™ HD Array includes a total of approximately 6.5 million probes: 1 probe per allele in triplicate for 750,000 SNPs probes and 1.9 million non-polymorphic probes.

Answer Id: E13834

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