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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.

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Product FAQ

Are there any service providers for the Axiom Genome-Wide BOS 1 Array Plate?

Answer

A number of service providers have experience running the Axiom Assay and the genotyping call algorithm that is used with the Axiom Genome-Wide BOS 1 Array Plate.

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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.

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Product FAQ

What is the recommended sequence format for uploading into the Probe Match tool?

Answer

You may paste or upload sequences in FASTA format for analysis with the Probe Match tool (https://tools.thermofisher.com/content/sfs/manuals/probematch_manual.pdf). Please note: You may also paste sequence without any header information.

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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.

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Product FAQ

How should I isolate/purify my RNA for miRNA array analysis?

Answer

Any kit for purification of total RNA or LMW (Low Molecular Weight) RNA will be compatible with FlashTag Biotin HSR. Elute or resuspend the RNA in nuclease-free water. Ensure that the purification method retains low molecular weight species. Some commercial products that have been tested successfully with FlashTag Biotin HSR include:

mirVana miRNA Isolation Kit
RecoverAll Total Nucleic Acid Isolation Kit for FFPE
PureLink miRNA Isolation Kit
TRIzol reagent (total RNA only) with additional overnight -20 degrees C precipitation step during isopropanol precipitation.

Answer Id: E14047

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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).

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Product FAQ

How do I correlate the SNPs on the mapping GeneChip array with this design?

Answer

Associations between SNPs and exon probe sets can be obtained by using genome assembly position information which is provided for both the mapping array and the exon array. One useful tool for doing this is the UCSC Table Browser at http://genome.ucsc.edu/cgi-bin/hgTables.

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Product FAQ

How should the thermal cycler settings be programmed for use with the CytoScan 750 array?

Answer

  Applied Biosystems Veriti 96-well Bio-Rad DNA Engine PTC-200 Eppendorf Mastercycler Pro S
Lid temperature 103 degrees C 103 degrees C 103 degrees C
Temperature mode N/A Calculated Safe
TSP heated lid N/A N/A Yes
Switch off lid at a low block temperature N/A N/A No

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Product FAQ

What can cause MAPD failures when using the CyotScan Assay?

Answer

MAPD failures can be caused by assay drift due to variation in assay execution or over fragmentation. See the troubleshooting section of the CytoScan Assay User Manual (Cat. No. 703038, https://tools.thermofisher.com/content/sfs/manuals/cytoscan_assay_user_manual.pdf) for more information.

Answer Id: E13934

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Product FAQ

What is the difference between a PSR and an Exon?

Answer

PSR is the smallest unit on the exon array for expression profiling and each PSR is represented by an individual probe set. In some cases, each PSR is also an exon; in other cases, due to variation in overlapping exon structures, the PSR can be a subset of the true biological exon. As a result, alternatively spliced exons from the same gene may overlap (i.e., alternative donor or acceptor site); however, PSRs have the property that they do not overlap each other in the genome space, except if annotations change with a newer version of the genome assemblies. In cases where multiple annotations infer different exon structures, that one exon cluster (a group of overlapping exons) will be divided into multiple PSRs. Therefore, in the final design, there are approximately 1,000,000 exon clusters represented by approximately 1,400,000 PSRs.

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Product FAQ

Can I upload or paste multiple DNA sequences into the Probe Match tool?

Answer

Yes, you can upload or paste a text file into the Probe Match tool with multiple sequences in FASTA format. Please note: The size of the uploaded file must not exceed 20 KB. (To determine the file size on a Windows-based system, right-click the text file icon, and select the "Properties" option).

Answer Id: E13635

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Product FAQ

Can I buy just the reagents or arrays alone instead of the CytoScan Reagent Kit?

Answer

No, the reagents and arrays are sold as bundles for 24 reactions (Cat. No. 901835)

Answer Id: E13959

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Product FAQ

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

Answer

Either total RNA or low melecular weight (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

Are there any articles that describe miRNA Array data analysis?

Answer

F Sato. Intra-Platform Repeatability and Inter-Platform Comparibility of microRNA microarray technology. PLoS ONE May 2009, volume 4, issue 5, e5540.
D Sarkar. Quality Assessment and data analysis for microRNA expression arrays. Nucleic Acids Research 2009, vol. 37, no. 2, e17 (doi: 10.1093/ner/gkn932).

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