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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

Can I use the human, mouse, and rat .ps files to limit my data output in Partek Express and Partek Genomics Suite?

Answer

No, Partek Express and Partek Genomics Suite do not use the .ps file when analyzing data. We will notify you when this has been resolved.

Answer Id: E14127

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Product FAQ

Which software supports the Fluidics Station 400 and Agilent Technologies' GeneArray 2500 Scanner?

Answer

GCOS is the software that provides instrument control for the Fluidics Station 400 and GeneArray 2500 Scanner. GCOS, FS400, and GA2500 are discontinued products. For upgrade information, please contact your technical support team.

Answer Id: E14218

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Product FAQ

What are the features of GCOS and GCOS Server?

Answer

Please see the features below for MAS, GCOS Client, or GCOS Server:

Instrument Control / Data Acquisition +, +, -
Gene Expression Data Analysis (Statistical Algorithm (CHP) +, + ,+
Manage & Associate Projects, Experiments, Samples & Data -, +, +
Publishing to AADM Database -, +, +
MIAME Standard Template -, +, +
Barcode Support, Automation -, +, ++
User Access, Roles, Security -, -, +
Centralized Data Sharing -, -, +

Answer Id: E14175

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Product FAQ

How does the protocol for WT Sense Target Labeling assays perform on partially degraded samples?

Answer

Utilizing the WT assay for partially degraded samples may be an attractive strategy for profiling these samples. However, it has not been tested thus far in development; therefore, it is recommended that only high-quality total RNA samples should be used.

Answer Id: E13656

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Product FAQ

Why do I need to use GeneChip 20X Hybridization Controls?

Answer

The Hybridization Controls are high-quality controls for monitoring array hybridization, washing, and staining for reproducible results.

20X Hybridization Controls are composed of a mixture of biotinylated and fragmented cRNA of bioB, bioC, and bioD from E. coli and cre from P1 bacteriophage in staggered concentrations. The premixed controls are ready to be added directly to the hybridization cocktail. Probes for detecting these controls are present on GeneChip miRNA Array, ThermoFisher Scientific miRNA Array Strip, and Thermofisher Scientific miRNA Array Plate.

The 20X Hybridization Controls are spiked into the hybridization cocktail, independent of RNA sample preparation, and are thus used to evaluate sample hybridization efficiency on eukaryotic gene expression arrays. As the 20X Hybridization Controls are used to troubleshoot potential array and array processing issues, a failure to include the 20X Hybridization Controls in the hybridization cocktail will void the customer's ability to submit an array replacement request.

Answer Id: E14128

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Product FAQ

What is the web server in Command Console Software used for?

Answer

Command Console Software is provided in two forms: Standalone Edition and Workgroup Edition. The Standalone Edition has the appearance of a desktop application, although it uses a local web server and provides certain functionality through a web interface (web pages). The Workgroup Edition adds the Microsoft IIS Web Server to the configuration, allowing for cross-platform and remote access to many Command Console functions.

Answer Id: E14219

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Product FAQ

What about data compatibility between MAS v.5.1 and GCOS v.1?

Answer

We have maintained full forward and backward data compatibility between GCOS v.1 and MAS v.5.1. The following summarizes file compatibility between the two software products.

MASGCOS ClientGTYPE/GSEQ
Create:Create:Create:
DATDATCHP (DNA analysis)
CELCELFASTA
CHPCHP (expression)
EXPCAB (export)
RPT, TXTRPT, TXT (export)
Analyze:Analyze:Analyze:
DATDATCEL (GCOS)
CELCEL

Answer Id: E14176

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Product FAQ

What is the difference between GeneChip miRNA Array, miRNA Array Strip, and miRNA Array Plate?

Answer

The only difference is the form factor of the array. The arrays have the exact same design and contain the same number of probes and probe sets.

Answer Id: E14140

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Product FAQ

What is the recommended hybridization time for Affymetrix miRNA Array Plates?

Answer

The recommended hybridization time is 17 ± 1 hour.

Answer Id: E14119

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Product FAQ

What is the concentration of Vial 10, ELOSA positive control?

Answer

0.25 ng/µL

Answer Id: E14064

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Product FAQ

Why is there no pre-hybridization step for the arrays using the targets from the WT Assay?

Answer

The pre-hybridization step was required for the 3' target in the GeneChip IVT Assays.

No pre-hybridization step is necessary for the WT targets. There are many differences between the WT targets and the 3' targets in terms of the nature of the molecules (DNA vs. RNA), as well as labeling molecule and hybridization cocktail makeup. It has been found that pre-hybridization is not necessary for the WT targets.

Answer Id: E13657

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Product FAQ

Where can I find the library files for Affymetrix miRNA Arrays ?

Answer

Access the library files on www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-data-analysis/genechip-array-library-files.html.

Answer Id: E14129

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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

Why must the PNA working solutions be discarded after one use when using the GeneChip Globin-Reduction Kit?

Answer

At this time we cannot recommend storage of the diluted PNA stock solutions due to the potential for the PNAs to aggregate, but we are investigating ways to do this in the future.

Answer Id: E13496

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Product FAQ

Are there any shutdowns run after bleaching the fluidics station when working with the CytoScan arrays?

Answer

Yes, it is recommended to run two water shutdown protocols after bleaching the fluidics station.

Answer Id: E13987

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Product FAQ

What does the "_s_at" extension represent in the HG-U133 probe set name?

Answer

The primary goal in probe set selection is to select a probe set unique to a single transcript or common among a small set of similar transcript variants. A probe set name is appended with the "_s_at" extension when all the probes exactly match multiple transcripts. The probe set selection process generally favors probe sets measuring fewer transcripts. Probe sets with common probes among multiple transcripts (the "_s_at" probe sets), are frequent and are to be expected, due to alternative polyadenylation and alternative splicing. In most cases, "_s_at" probe sets represent transcripts from the same gene, but the same probe set can sometimes also represent transcripts from homologous genes. One transcript may be represented by both a unique and an "_s_at" probe set when the transcript variation is sufficient.

Answer Id: E14178

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Product FAQ

What data files are produced during the assay and analysis process?

Answer

These data files are produced that are key to the process:

ARR file - This file includes sample information.
AUDIT file - This file is a log of the sample history.
DAT file - This file is the raw data from the scanner.
CEL file - This file is the gridded and processed data.
xxCHP file - This file is the output of ChAS 3.1 and contains all of the analysis data.
CHPCAR file - This file stores user-annotated calls, interpretations, and modifications made to CHP file segment data (ChAS v2.0 and higher).

Answer Id: E13867

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Product FAQ

My RNA sample contains EDTA. Can I use it for FlashTag labeling?

Answer

The maximum amount of EDTA in a sample, prior to FlashTag labeling, can be 0.1-1mM. If more EDTA is present, the sample should be desalted/precipitated or purified prior to FlashTag labeling.

Answer Id: E14052

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Product FAQ

What is the maximum number of freeze/thaw cycles recommended for the CytoScan Reagent kit?

Answer

The CytoScan Reagent kit has been validated for less than or equal to 5 freeze/thaw cycles.

Answer Id: E14279

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Product FAQ

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

Answer

No, the CEL files from GeneChip miRNA Array, Thermo Fisher Scientific miRNA Array Strip, and miRNA Array Plates are not compatible.

Answer Id: E14141

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Product FAQ

What is the probe interrogation position?

Answer

The probe interrogation position indicates the base position on the consensus/exemplar sequence where the central base of the probe aligns, which is the 13th base of a 25mer probe.

Answer Id: E14283

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Product FAQ

What is the fluidics protocol for the GeneChip Rat Expression Set 230?

Answer

FS450_0004 when using the Hybridization, Wash and Stain Kit.

Answer Id: E13803

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Product FAQ

What is the impact of the lower number of SNPs on the coverage when using the Genome-Wide Human SNP 5.0 assay?

Answer

The Mapping 500K has a high level of redundancy, and numerous studies have shown that dropping 10% of the SNPs will not significantly impact LD coverage. This data is show in the Barrett and Cardon Nature genetics paper. Any minor loss in LD coverage is more than compensated for by the increased power from running more samples. For the HapMap CEPH samples, there is a 2% difference LD coverage, when measured at an R2 = 0.,8 between the 500K and the SNP 5.0

Answer Id: E13741

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Product FAQ

How do I know if my first-cycle cDNA synthesis reaction has worked well?

Answer

It is challenging to assess the success of the cDNA synthesis reaction and this applies to both the One-Cycle and Two-Cycle protocol. This is because the amount of double-stranded cDNA obtained is quite small, and it is mixed in with the starting total RNA materials. The best way to QC this step is to carry out the subsequent IVT reaction and quantitate the cRNA yield. [This answer refers to a product that has been discontinued.]

Answer Id: E14368

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Product FAQ

What does the percentage of aberrant cells mean?

Answer

This represents the percentage of aberrant cells in a sample:

When reported as “N/A,” it means that the percentage of aberrant cells could not be estimated.
When reported as a percentage (e.g., 60%), it means that 60% of the cells were aberrant.

Answer Id: E13859

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Product FAQ

Which QC methods for copy number analysis are available in GTC 4.2?

Answer

-SNP Array 6.0: Median Absolute Pairwise Difference (MAPD)
-100K Set/500K Array Set: Interquartile Range (IQR)

Answer Id: E13685

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Product FAQ

For the Affymetrix Mouse Diversity Genoytping Array, how were SNPs selected ?

Answer

SNPs were selected to represent polymorphisms from a comprehensive set of common inbred laboratory and wild-derived mice. For additional information, please see “A customized and versatile high-density genotyping array for the mouse” (Yang H., et al., Nature Methods, 2009).

Answer Id: E14146

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Product FAQ

I have labeled my samples with FlashTag labeling kit, but I am not ready to hybridize the miRNA Arrays. What should I do?

Answer

Store the biotin-labeled RNA samples on ice for up to 6 hours, or at -20 degrees C for up to two weeks.

Answer Id: E14065

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Product FAQ

Does Thermo Fisher Scientific provide services for running GeneChip expression arrays for customers?

Answer

No, Thermo Fisher Scientific does not provide any services for running these arrays. However, several service providers provide GeneChip analysis for a fee.

Answer Id: E13581

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