You searched for: 

genechip products

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

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How do I obtain the new stain-dispensing script?

Answer

If you plan to use the stain-dispensing script, please contact your local field support specialist to have it installed or email us at techsupport@thermofisher.com.

Answer Id: E13790

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

When would we choose normal diploid analysis over single-sample analysis?

Answer

The normal diploid analysis for a CytoScan HD and 750K array is recommended for cancer samples in which greater than 50% of the genome is likely to be rearranged. This analysis automatically determines the normal diploid regions and normalizes the rest of the samples based on those regions, resulting in properly centered data. The normal diploid analysis is NOT recommended for CytoScan Optima Array.

For samples run through the normal single sample analysis, the following QC metrics are recommended:
MAPD less than 0.25
SNPQC OR ndSNPQC greater than or equal to 15
Waviness-SD OR ndwavinessSD less than 0.12

Answer Id: E13848

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Which format is the CytoScan XON array?

Answer

It is a 49 format array.

 

Answer Id: E16630

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Do I have to use the new stain-dispensing script?

Answer

No. The new stain-dispensing script was designed to increase productivity and reduce the chance of error during pipetting of the stains. However, some may feel more comfortable dispensing stains by hand. For manual and automated stain-dispensing procedures, please consult the latest version of the GeneChip Expression Analysis Technical Manual for HT Array Plates Using the GeneChip Array Station (https://tools.thermofisher.com/content/sfs/manuals/gcas_ht_plate_manual.pdf - login required).

Answer Id: E13791

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What is the total number of probes in OncoScan CNV Plus Assay Kit?

Answer

OncoScan CNV Plus Assay Kit has 217,454 probes.

Answer Id: E13849

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Is the Command Console web server hosted by customers or by your company?

Answer

The Command Console web server is hosted by the customer.

Answer Id: E14220

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What are the quality requirements for genomic DNA for a successful run on a CytoScan array?

Answer

Sample must be double-stranded genomic DNA (gDNA) that is not degraded (size 10 kb by gel analysis), not contaminated, and free of PCR inhibitors. Sample should be diluted to 20 ng/µL in low-EDTA TE buffer.

 

Answer Id: E16631

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How many freeze/thaw cycles are validated for CytoScan Reagent Kit (24 samples)?

Answer

CytoScan Reagent Kit (Cat. No. 901808) is validated for for 4 in-use freeze/thaw events but have to use the kit within a month (30 days) once opened even if they have not gone through 4 freeze-thaws.

Answer Id: E13951

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Can I hybridize the DNA target to the HG-U133 arrays?

Answer

The WT Plus Assay is optimized to produce targets specifically for hybridization to the Whole Transcriptome(WT) type of design. The target is in the sense orientation and the GeneChip Human Genome U133 Plus 2.0 Array is designed to be compatible with anti-sense targets. Therefore, it is not recommended to mix and match the assays and the array types.

Answer Id: E13654

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What is the threshold for the Contrast QC metric for the SNP Array 6.0?

Answer

The Contrast QC threshold is 0.4 or greater. The overall quality of the data set is assessed by measuring the average Contrast QC for all passing samples. The average Contrast QC for all passing samples should be 1.7 or greater.

Answer Id: E13680

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How are sno/sca and hairpin probe sets selected and how does that impact my signal summarization?

Answer

Probes for snoRNA, scaRNA, and hairpins are selected to maximize probe response to target concentration in the sample while minimizing cross-hybridization to other potential targets in the sample. In order to minimize cross-hybridization, potential targets are inferred from the landscape of known sequences from the input dataset and used in a filtering process called pruning which penalizes probe candidates that may cross-hybridize to unwanted targets. As the landscape of known sequences improves, we can improve our pruning set to avoid probe candidates previously thought to be unique. An improved pruning set will reduce the chances a probe will cross-hybridize to unwanted target, improving the probe set representation of the intended target. As a result of the improved probe selection, few probe sets are required to represent the same number of sequences.

Answer Id: E14145

Was this answer helpful?

Yes
No
Thank you for your response

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

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How should I quantitate my DNA for the OncoScan assay?

Answer

Sample concentration for the OncoScan assay must be performed using a dsDNA specific quantitation method. We strongly recommend using either Quant-it PicoGreen Assay or Qubit dsDNA quantitation kit. Sample concentration determined by UV absorbance or NanoDrop must NOT be used at all in this assay.

Answer Id: E14273

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How many probes are SNPs in the OncoScan CNV Plus Assay kit?

Answer

Virtually all probes in OncoScan CNV Plus Assay Kit are SNPs. There are a few thousand probes that are not polymorphic.

Answer Id: E13850

Was this answer helpful?

Yes
No
Thank you for your response