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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

What is the Canary algorithm?

Answer

Copy number polymorphism (CNP) analysis is performed using the Canary algorithm. Canary was developed by the Broad Institute for making copy number state calls in genomic regions with copy number polymorphisms. CNP analysis using Canary is supported in GTC 3.0.1 for the SNP Array 6.0. See Appendix G in the GTC 3.0.1 User Manual for more information on CNP analysis and the Canary algorithm.

Answer Id: E13570

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Product FAQ

Should I enrich my total RNA for miRNA for downstream array analysis?

Answer

Either Total RNA or LMW RNA can be labeled with FlashTag™ Biotin HSR. Using total RNA can save time and money, and prevent sample loss.

Answer Id: E14048

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Product FAQ

Which RefSeq version is provided with the browser for displaying probe annotation?

Answer

The RefSeq data provided with the bowser is for genome version hg18, dated October 22, 2007.

Answer Id: E13571

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Product FAQ

What components does the GeneChip™ Two-Cycle cDNA Synthesis Kit contain?

Answer

The Two-Cycle cDNA Synthesis Kit contains all necessary reagents (see the following table) to carry out the two cycles of cDNA synthesis for thirty samples. Note that the reagents for the intermediary in vitro transcription (IVT) amplification using un-labeled ribonucleotides, between the two cDNA synthesis reactions, is not included in the kit. The Ambion MEGAscript T7 Kit is recommended.

Component Name: Concentration: Volume: Quantity
T7-Oligo(dT) Primer, 50 μM: 50 μM: 120 μL: 1
5X 1st Strand Reaction Mix: 5X: 180 μL: 1
DTT, 0.1M: 0.1M: 90 μ:L 1
dNTP, 10 mM: 10 mM: 200 μL: 1
SuperScript™ II: 200 U/μL: 60 μL: 1
RNase Inhibitor: 40 U/μL: 45 μL: 1
5X 2nd Strand Reaction Mix: 5X: 900 μL: 1
Random Primers: 3 μg/μL: 60 μL: 1
MgCl2, 1M: 1M: 60 μL: 1
E.coli DNA Polymerase I: 10 U/μL: 200 μL: 1
RNase H: 2 U/μL: 55 μL: 1
T4 DNA Polymerase: 5 U/μL: 60 μL: 1
RNase-free Water: n/a: 9.5 mL: 1

Answer Id: E14170

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Product FAQ

Can I open two files that have been analyzed with different NetAffx™ versions at the same time in the ChAS 3.1 browser?

Answer

The ChAS 3.1 browser allows for loading of different NetAffx versions at the same time (only if the versions are from all the same reference and genome builds).

The ChAS 3.1 browser cannot load NetAffx versions from different genome builds (Hg18 and Hg19) or from an external reference version (dbSNP build 135 and dbSNP build 132).

Answer Id: E13872

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Product FAQ

How many and what species are not detected by the Axiom™ Microbiome Array?

Answer

81 species are not detectable on Axiom™ Microbiome Array. For a complete list of species not detected, please contact the Technical Support Team.

Answer Id: E14305

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Product FAQ

How should I quantitate my RNA for downstream array analysis?

Answer

To accurately determine the concentration of the RNA sample, we recommend Quant-iT™ RiboGreen RNA Assay Kit (Cat. No. R11490) or the NanoDrop™ ND-1000 Spectrophotometer.

Answer Id: E14049

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Product FAQ

Which transcripts that were represented on the MG-U74v2 Set are not represented on the GeneChip™ Mouse Expression Set 430?

Answer

Users can access comparison spreadsheets (link) to evaluate the relationships between probe sets on the previous and current designs. There are 41 probe sets from the MG-U74v2 Set that have no representative probe sets on the Mouse Set 430. These are listed in the spreadsheet titled "None". For further explanation on the use and contents of the comparison spreadsheets on the web site.

Answer Id: E13734

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Product FAQ

Should I expect the same performance between user-prepared and HT HWS reagents?

Answer

The HT HWS reagents have been rigorously tested and validated at Affymetrix™ to perform to our system specifications. Data from GeneChip™ HT Array Plates processed with HT HWS Kit reagents showed similar data and results to HT Array Plates processed with manually prepared reagents. For sample data obtained from plates processed with both methods, please visit www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-data-analysis/microarray-analysis-sample-data.html

Answer Id: E13792

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Product FAQ

How can I determine the limit of detection?

Answer

In Partek, the limit of detection = 2 Standard Deviations over background. In miRNA QC Tool, click 2X to subtract the background. At this point, anything above background (as defined by the project description table) is significant, if the p-value is also significant (as determined by the researcher).

Answer Id: E14090

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Product FAQ

What is the heat map viewer?

Answer

The heat map viewer allows users to compare the copy number variation (CNV) calls from CNVCHP files using raw intensity values from individual probe sets within the CNV regions from CNCHP files, and to survey large quantities of genomic data to detect de novo CNV regions.

The heat map viewer can display
Copy number intensity values (~log2 ratios) from probe sets in the CNCHP files alone, or with
Copy number state calls for the CNV regions in corresponding CNVCHP files.

Answer Id: E13572

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Product FAQ

How many bases can I resequence on a CustomSeq array?

Answer

Three formats of custom arrays are available that allow for the analysis of approximately 300kb, 100kb and 50kb of double stranded sequences. Please refer to the CustomSeq Design Guide for details on array content considerations. The exact maximum capacities are listed below.

Format: Maximum Capacity
49: 303,366
100: 117,254
169: 47,947

Answer Id: E14171

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Product FAQ

Can I track the samples that I have uploaded in the database?

Answer

If an xxCHP file has been previously published to the database, you will receive a warning indicating this sample already exists in the database. You can choose to overwrite the existing information or cancel to keep the existing information. 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 revisualize the results using the CYCHP/CHPCAR files.

Answer Id: E13886

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Product FAQ

Can custom annotation files be used for copy number analysis in GTC 3.0.1?

Answer

Yes, custom annotation files can be used for SNP genotyping and copy number analysis in GTC 3.0.1.

Answer Id: E13693

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