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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

The FlashTag HSR Range of Sensitivity is described in amoles; how does that translate to copies of microRNA?

Answer

The dynamic range of detection on a per molecule basis for any given miRNA is:

0.5 amoles = 300,000 copies
7400 amoles = 4,440,000,000 copies

Answer Id: E14058

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Product FAQ

What is Vial 3, ATP Mix in the FlashTag labeling kit?

Answer

Vial 3 contains 10mM ATP.

Answer Id: E14059

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Product FAQ

Are all PSRs represented by 4 probes?

Answer

About 90% of the exon-based probe sets contain 4 probes for each PSR. The remaining 10% are roughly equally split between 3, 2, and 1 probes for each probe set.

Answer Id: E13544

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Product FAQ

What is Vial 5, FlashTag Ligation Mix in the FlashTag labeling kit?

Answer

Vial 5 contains a proprietary 3DNA molecule conjugated with biotins. The 3DNA is attached to a poly(T) sequence that facilitates ligation to all poly(A)-tailed RNA molecules.

Answer Id: E14060

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Product FAQ

It seems that the probes may overlap heavily within a given PSR, how is this managed?

Answer

In many cases the Genechip probes do overlap quite heavily. Multiple probes, although overlapping, are utilized as they still provide separate physical measures of expression and add to the robustness of the platform. Care was taken to ensure that probes from the same probe set, however similar in sequence composition, are spatially separated on the array. In addition, the annotation library file contains information regarding how many independent probes there are, as well as the number of nonoverlapping probes, in each probe set. Independent probes are defined as those that have less or equal to 13 base overlaps with other probes in the probe set. This information provides additional insight and may be helpful to users when interpreting unexpected results.

Answer Id: E13546

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Product FAQ

What QC metrics will I use to assess the quality of my data?

Answer

Mean absolute relative log expression: MA (RLE)
-Detection of 20X spikes, Bio B, Bio C, Bio D & Cre
-House keeping controls
-Poly A controls
-Antigenomic GC - 12 background probes
-PM mean

Please refer to the QC Metrics for Human, Mouse and Rat HT PM Array Plates QRC for more information (http://tools.thermofisher.com/content/sfs/manuals/ hmr_qc_metrics_qrc.pdf).

Answer Id: E13604

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Product FAQ

What is Vial 8, RNA Spike Control Oligos in the FlashTag Labeling kits?

Answer

Vial 8 consists of five oligos which are spiked into the RNA sample prior to FlashTag labeling. These oligos contain controls for the GeneChip

miRNA array and the ELOSA QC Assay.
Oligos 2, 23, and 29 are RNA, and confirm poly(A) tailing and ligation.
Oligo 31 is poly(A) RNA, and confirms ligation.
Oligo 36 is poly(dA) DNA, and confirms ligation and lack of RNAses in the RNA sample.

The Affymetrix library file lists the following names for these probe sets:

spike in-control-2 st
spike in-control-23 st
spike in-control-29 st
spike in-control-31 st
spike in-control-36 st
Each probe set should show >1000 units or 9.96 for log2 signal (signal-background).

Answer Id: E14061

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Product FAQ

What type of alternative splicing events are you able to interrogate with this GeneChip array design?

Answer

The majority of the splicing changes occur because of alternative exon usage or exon skipping, which will be captured with this type of array design. Fine modifications such as alternative 5' or 3' splice site usage with shifts of less than 25 bases will not be captured by this design.

Answer Id: E13547

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Product FAQ

In the ELOSA, is mild shaking acceptable?

Answer

Mild shaking (50-300 RPM) is acceptable during sample hybridization and all other steps of the ELOSA, but is not required.

Answer Id: E14077

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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 is the hybridization temperature and rotation speed for CytoScan arrays?

Answer

The hybridization temperature is 50 degrees C. The rotation speed is 60 rpm.

Answer Id: E13983

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Product FAQ

For the CytoScan assay, does the expiration date apply to the date of opening or date of manufacturing?

Answer

The expiration date applies to the date of manufacturing. For the CytoScan Reagent Kit, it can be used for up to one year from the date of manufacturing.

Answer Id: E13907

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Product FAQ

If I have cartridges, can I move to PM only arrays in the middle of my project?

Answer

No, continue to finish products using the same procedures and products. New projects can be moved to PM only arrays.

Answer Id: E13605

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Product FAQ

What sample types are validated on the CytoScan assay?

Answer

The CytoScan assay has been validated with blood and cell line samples.

Answer Id: E13947

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