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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

Are the data obtained from the One-Cycle cDNA Synthesis Kit concordant with the previous "standard" GeneChip™ target labeling assay?

Answer

The One-Cycle cDNA Synthesis Kit is formulated following precisely the standard GeneChip™ target labeling assay and there is no change to the major reagents used in the protocol. Therefore, the performance of the assay and data obtained should be highly concordant. [This answer refers to a product that has been discontinued.]

Answer Id: E14355

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Product FAQ

Does the globin reduction procedure using the GeneChip™ Globin-Reduction kit affect the expression analysis of transcripts different from globin?

Answer

The PNA oligomers are highly specific for globin mRNA transcripts and do not hybridize stably to non-globin transcripts under the recommended conditions. Therefore, following hybridization of the PNAs and Oligo d(T) Promoter Primer, amplification and labeling of non-globin transcripts should be unaffected. Since the reduction of excess labeled globin transcript in the final cRNA product significantly reduces the globin cross-hybridization effects, GeneChip™ analysis will be more sensitive. As detection of transcripts expressed at lower levels will no longer be masked by excess globin cross-hybridization, and the relative expression levels on a gene-by-gene basis will be higher.

Answer Id: E13491

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Product FAQ

What are the Gene Ontology™ (GO) annotations? Are GO annotations provided for all GeneChip™ expression arrays?

Answer

The GO consortium (http://geneontology.org/) provides controlled vocabularies for the description of the molecular function, biological process, and cellular component of gene products. Currently, GO classifications are available for the Human (U133, U95, HuGeneFL, HC-G110), Murine (U74, Mu11k, Mu19k), Drosophila, Arabidopsis, and Yeast GeneChip™ arrays.
The Analysis Center also provides hyperlinks to the AMIGO and QuickGO browsers, enabling you to view the complete hierarchy for all the GO terms associated with the probe sets.

Answer Id: E13469

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Product FAQ

Which assay do you recommend for use with Affymetrix™ GeneChip™ miRNA Arrays?

Answer

Affymetrix™ only supports use of the Affymetrix™ FlashTag™ Biotin HSR RNA Labeling Kit for preparing targets to be applied to GeneChip™ miRNA Array, Affymetrix™ miRNA Array Strip, and Affymetrix™ miRNA Array Plate. This product may be ordered through Affymetrix™ using Cat. No.s 901910 for the 10- reaction kit and 901911 for the 30-reaction kit.

Answer Id: E14124

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Product FAQ

What are the major differences and improvements comparing the new Two-Cycle cDNA Synthesis Kit with the Affymetrix™ Small Sample Target Labeling Version II Protocol?

Answer

The Two-Cycle cDNA Synthesis Kit was developed primarily based on SSTLvII, with some additional optimization focusing on a more streamlined procedure. More information on these changes is summarized as follows:
The new Two-Cycle cDNA Synthesis Kit protocol utilizes larger reaction volume for the 1st-cycle cDNA synthesis step, allowing more flexibility in the starting material concentration and reducing potential pipetting variations.
The new Two-Cycle cDNA Synthesis Kit protocol eliminates the cDNA cleanup step in the 1st cycle, increasing ease of use.
The GeneChip™ Sample Cleanup Module is used for all cDNA and cRNA cleanup steps, replacing all previously recommended precipitation or speed vacuum protocols.
Overnight incubations are recommended for both IVT steps following the 1st- and 2nd-cycle cDNA synthesis, reducing the total target labeling time to 2½ days. [This answer refers to a product that has been discontinued.]

Answer Id: E14360

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Product FAQ

Does this Two-Cycle cDNA Synthesis Kit/protocol work well on partially degraded RNA samples?

Answer

No. Similar to previous recommendations for the standard protocol and SSTLvII, the Two-Cycle cDNA Synthesis Kit protocol also requires high-quality total RNA as starting material. Most commonly, customers assess OD260/280 ratios together with electrophoretic analysis results when sufficient material is available. When sample quantity is limiting, the combination of RiboGreen for quantitation and Bioanalyzer for quality assessment has worked quite well. To better distinguish whether the starting material quality has affected the target labeling process, it is recommended to use the GeneChip™ Eukaryotic Poly-A RNA Control Kit and spike the positive controls into the starting materials for efficient troubleshooting. [This answer refers to a product that has been discontinued.]

Answer Id: E14363

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Product FAQ

Which assay do you recommend for use with Affymetrix™ miRNA Array Plates?

Answer

We only support use of the Affymetrix™ FlashTag™ Biotin HSR RNA Labeling Kit for preparing targets to be applied to GeneChip™ miRNA Array, Affymetrix™ miRNA 3.1 Array Strip, and Affymetrix™ miRNA 3.1 Array Plate. This product may be ordered using Cat. No. 901910 or 901911.

Answer Id: E14110

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Product FAQ

How does your Two-Cycle cDNA Synthesis Kit protocol perform compared with Ambion's MessageAmp Kit or Arcturus's RiboAmp Kit?

Answer

GeneChip™ assays are an integrated part of the complete system solution and are the only reagent kits developed and fully validated on GeneChip™ brand arrays. With a thorough understanding of the performance characteristics of the GeneChip™ reagent kits on GeneChip™ arrays, users should have more confidence in obtaining meaningful results. Affymetrix™ has been very diligent in investigating alternative target labeling protocols to ensure that researchers have access to the most robust and standardized assays when running GeneChip™ arrays. Affymetrix™ believes that the current set of GeneChip™ reagents are the most optimized solutions and can help customers extract the most reproducible and reliable data on GeneChip™ arrays. Affymetrix™ will continue to research alternative procedures to evolve the assay for improved ease of use and more streamlined assays. [This answer refers to a product that has been discontinued.]

Answer Id: E14364

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Product FAQ

Why are you recommending the overnight incubation for the IVT reaction?

Answer

There are two major benefits for this change in protocol. One benefit is that it provides the option for starting with as little as 1 µg of total RNA using just the standard One-Cycle Labeling protocol. The other benefit is that it incorporates a more convenient and efficient experimental workflow.

Previously, IVT was carried out with 4-5 hours of incubation on the second day of a standard One-Cycle Target Labeling protocol. This made the procedure on the second day rather hectic, since users typically performed the cRNA cleanup (~30 minutes) and fragmentation (~1 hour) after the IVT in order to hybridize their samples on the arrays overnight.

In order to make the workflow more flexible, the new GeneChip™ IVT Labeling Kit provides a general guideline of using an overnight incubation. However, for customers who prefer the previous protocol, they have the option to spike in additional T7 RNA Polymerase (Ambion, P/N 2085, as described in the product insert) to reduce the IVT reaction time to 4-5 hours.

Answer Id: E13607

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Product FAQ

Why are there more data headers and columns in my miRNA 4.0/4.1 or newer annotation files?

Answer

The miRNA 4.0/4.1 annotations contain additional data fields to help ease the integration and correlation of small non-coding RNA data contained on Affymetrix™ miRNA 4.0 and 4.1 Arrays (and newer) with the content from our other expression products such as GeneChip™ Human Genome U133 Plus 2.0 Array, GeneChip™ Human Gene 2.0 ST Array, and GeneChip™ Human Transcriptome Array 2.0. These additional fields include:

- Genomic context (where the miRNA is located in the genome)
- Clustered miRNA (miRNA that are located 10 KB from one another)
- Predicted miRNA targets
- Validated miRNA targets

Answer Id: E14123

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Product FAQ

I have never performed any small sample target labeling before. Do you have any suggestions for incorporating the Two-Cycle cDNA Synthesis Kit into our routine GeneChip™ microarray analysis?

Answer

The basic principles of the Two-Cycle Target Labeling Assay are very similar to the One-Cycle Standard Protocol, and many of the steps involved may look familiar. However, since it does require manipulation of very small amounts of materials in the 1st cycle, even the most experienced GeneChip™ microarray users may not obtain ideal data when using the Two-Cycle protocol the first time. Therefore, it is suggested that users first read the protocol very carefully, including all notes and tips, and then practice initially with diluted samples that you have previously characterized using the One-Cycle Standard Protocol. This way, you will be starting with materials of good quality and you already know what results to anticipate. Follow common laboratory practices that minimize RNase contamination and use caution at each step to prevent sample loss. [This answer refers to a product that has been discontinued.]

Answer Id: E14362

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Product FAQ

What is your reproducibility on GeneChip™ CustomSeq arrays?

Answer

>99.99%, as with all GeneChip™ products, CustomSeq arrays provide extremely reproducible data. Capillary sequencing data varies greatly depending on the expertise of the lab. For technical details, please refer to the GeneChip™ CustomSeq Resequencing Array Base Calling Algorithm Version 2.0: Performance in Homozygous and Heterozygous SNP Detection (https://tools.thermofisher.com/content/sfs/brochures/customseq_arraybase_technote.pdf) technical note.

Answer Id: E13509

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Product FAQ

Which RNA isolation method do you recommend for the Two-Cycle cDNA Synthesis protocol?

Answer

Different tissue types may have different requirements for RNA extraction. Several commercial kits and protocols are currently available for total RNA isolation from small samples (tissues, biopsies, LCM samples, etc.). Select the one that is most suitable for the processing of your samples and follow the vendor-recommended procedures closely. Assess the quality and integrity of obtained total RNA samples carefully by gel electrophoresis or Bioanalyzer before starting the GeneChip™ target labeling protocol. [This answer refers to a product that has been discontinued.]

Answer Id: E14366

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Product FAQ

What is the detection sensitivity of the Two-Cycle cDNA Synthesis Kit protocol?

Answer

One way to assess the assay sensitivity is to monitor the global array metric of percent Present calls. From the same high-quality starting material, the Two-Cycle cDNA Synthesis protocol demonstrates highly comparable P% calls as the results generated from the One-Cycle cDNA Synthesis protocol. Another way to estimate the detection sensitivity is to use poly-A RNA spike-in controls. Following the recommended protocol included in the GeneChip™ Eukaryotic Poly-A RNA Control Kit, the Two-Cycle cDNA Synthesis Kit generally amplifies the samples sufficiently to detect the 3'-Probe Set of lys (the transcript with the lowest concentration, at 1:100,000 complexity ratio) as Present over 70% of the time. [This answer refers to a product that has been discontinued.]

Answer Id: E14365

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