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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

Why are the probes on the DMET Plus Array different lengths?

Answer

Different probe lengths can help differentiate alleles when the GC content varies. Since we are using a single condition for hyb and wash, it is difficult to optimize across a wide range of GC content. So for example if a SNP is in a sequence that is high GC, a shorter probe (23 or 21 mer) might improve allelic discrimination. If the SNP is in an AT rich sequence and has an overall lower Tm, then a slightly longer probe could improve discrimination.

Answer Id: E14291

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Product FAQ

What sample populations and criteria were used to select the markers for DMET Plus Array?

Answer

We used multiple populations (HapMap and Extended HapMap) when building the large internal reference set. The actual SNPs that are on the array come largely from the literature and we are unaware of any population bias that is in this collection. Much of the content did in fact come from the Pharma ADME web site. This consortia assembled a list of markers in genes that were prioritized into different classes. The most important of these is referred to as Core markers which mean that they have been validated in the scientific literature as having clinical relevance in drug responses. Markers were reviewed with several Pharmaceutical companies as well for input on important ADME markers.

Answer Id: E14292

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Product FAQ

What 3'/5' ratio for control genes, for example GAPDH and Actin, should I anticipate to obtain on GeneChip probe arrays?

Answer

In addition to the conventional probe sets designed to be within the most 3' 600 bp of a transcript, additional probe sets in the 5' region and middle portion (M) of the transcript have also been selected for certain housekeeping genes, including GAPDH and Actin. Signal intensity ratio of the 3' probe set over the 5' probe set is often referred to as the 3'/5' ratio. This ratio gives an indication of the integrity of your starting RNA, efficiency of first strand cDNA synthesis, and/or in vitro transcription of cRNA. The signal of each probe set reflects the sequence of the probes and their hybridization properties. A 1:1 molar ratio of the 3' to 5' transcript regions will not necessarily give a signal ratio of 1.

There is no single threshold cutoff to assess sample quality for all of the diverse organisms and tissues. This is due to the presence of different isoforms of these house-keeping genes and their different expression patterns in various tissues and organisms. Although we routinely refer to a threshold ratio of less than 3 for the most common tissues, such as mammalian liver and brain, this may not be applicable to all situations. It may be more appropriate to document the 3'/5' ratios within a particular study and flag the results that deviate, therefore representing an unusual sample that deserves further investigation.

Answer Id: E13597

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Product FAQ

What is the correct fluidics script for CytoScan HD Array?

Answer

The correct fluidics script is CytoScanHD_Array_450.

Answer Id: E13992

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Product FAQ

On average, how many probes are used to represent a corresponding GeneChip Human Genome U133 (HG-U133) Array probe set where there are 11 probe pairs?

Answer

The majority of the HG-U133 Plus 2.0 Array consensus sequences are well covered in the new design with approximately 75% of them containing over 8 probes on the Exon Array. The remaining 25% have less overlap with the new exon probes, and are mostly attributed to EST-based HG-U133 Array probe sets that do not contain an annotated coding region. As a result, in many such cases, the entire HG-U133 Array EST-based consensus sequence is designated as one PSR, with around 4 probes selected for that entire region.

Answer Id: E13664

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Product FAQ

How is gender determined/called in DMET Console?

Answer

In DMET console, gender calls can be found by looking at the CHP summary table, “Show All Columns”. Column “cn-probe-chrXY-ratio_gender_ratio”, shows how clearly a sample was called male or female. If this ratio is at least 0.68, it's called “male”. If this ratio is no more than 0.17, it's called “female”. This is basically a ratio of average raw signal of selected X and Y chromosome probesets and is performed on raw signal data, independent of genotyping method.

Answer Id: E14293

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Product FAQ

Which fluidics protocol should I use when processing a Gene 1.0 ST Array?

Answer

FS450_00007 should be used when processing Gene 1.0 ST Array. Up-to-date fluidics scripts can be obtained from the website.

Answer Id: E14097

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Product FAQ

Can array results from different laboratories and different times be compared with each other directly and how do you control the variables in this type of experiment?

Answer

Array results can potentially be compared directly. However, it is important to check the following important elements before doing so:

-Experimental design strategy should be the same at various sites.
-Identical target labeling protocols should be followed, and yields from cDNA and IVT reactions should be within the same range as specified for that study.
-Same algorithm parameters should be used.
-Similar results from 3'/5' ratios, background, noise, and scaling factors. Check arrays for scratches and even hybridization/staining.
-Comparability of results obtained from different operators should be evaluated before including their results in the same study.

Answer Id: E13598

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Product FAQ

What file sizes are associated with CytoScan HD Array?

Answer

The CEL file is ~66 MB, and the CYCHP file is ~119 MB.

Answer Id: E13993

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Product FAQ

Will SST-RMA be available in APT?

Answer

Yes, the SST-RMA analysis algorithm will be available in APT.

Answer Id: E14023

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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.

Answer Id: E13536

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Product FAQ

How often do I need to do maintenance on the fluidics station?

Answer

With normal use (e.g., 20 arrays/module/week), we recommend the following schedule: Every week, the needle bleaching protocol (i.e., "Bleach" fluidics protocol) should be performed; on a monthly basis, the full-fluidics bleaching protocol (i.e., "Monthly Decontamination" protocol) should be performed and the peristaltic-pump tubing replaced. Please refer to Section 4, Fluidics Station Maintenance Procedures, for more detail.

Answer Id: E13665

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Product FAQ

Can the input material be polyA RNA or mRNA instead of total RNA for microarray studies?

Answer

While mRNA should yield good results, we have not validated the product for use outside of total RNA. If you wanted to use mRNA, you will have to do some optimization to determine the correct amount of input material.

Answer Id: E14310

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Product FAQ

How many times can the DMET Reagents be used/how many freeze/thaws?

Answer

The DMET Plus Reagents are for single-use only. Do not thaw and refreeze reagents. This information is also available on the package insert of the reagents.

Answer Id: E14294

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Product FAQ

Which fluidics protocol should I use when processing a Gene 2.0 ST Array?

Answer

FS450_00002 should be used when processing Gene 2.0 ST Array. Up-to-date fluidics scripts can be obtained from the website.

Answer Id: E14098

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Product FAQ

Is the PM only plate array content exactly the same as the cartridge?

Answer

No, the PM only arrays have probes that are perfect match only. The mismatch probes have been removed. For the HT HGU133 plus PM product roughly 3/4 of the probesets have 9 probes, a small portion has 10; the remaining probesets have 11. The Mouse and Rat PM only plate arrays utilize all 11 probes for each probeset.

Answer Id: E13599

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Product FAQ

What software is available for analysis for genoytping and copy number analysis?

Answer

All genotyping and copy number analysis is done with ChAS. CytoScan Cytogenetics Suite is not intended for genome-wide association studies.

Answer Id: E13995

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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

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Product FAQ

Does the ChAS database require an internet connection?

Answer

The ChAS server home page requires an active internet connection, which requires a web browser. (Chrome and Internet Explorer v11 are recommended.) If you are using the local ChAS DB, an active internet connection is not required.

Answer Id: E13885

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Product FAQ

What is the hybridization volume recommended for Thermo Fisher Scientific miRNA Arrays?

Answer

GeneChip miRNA Array 130 µL of hybridization cocktail
Thermo Fisher Scientific miRNA Array Plates 120 µL of hybridization cocktail
Thermo Fisher Scientific miRNA Array Strips 120 µL of hybridization cocktail

Answer Id: E14137

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Product FAQ

When should data analyzed with RMA be re-analyzed using SST-RMA?

Answer

You should re-analyze your data if comparing with RT-PCR or RNA-Seq data using fold change values for filtering.

Answer Id: E14024

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Product FAQ

When I loaded the GeneChip Exon Array design information and array data into IGB, it seems that the probes were selected from outside of the RefSeq exons. Why?

Answer

The most likely explanation is that a different version of the genome assembly has been used to display the array design information and the array results. At launch, two versions of the library files are provided for array analysis corresponding to the Human Genome Build 34 and 35. Take care to use a consistent version number to match the array design with the actual array data for visualization in IGB.

Answer Id: E13537

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Product FAQ

Is there a possibility of contaminating the fluidics station with RNase when gene expression, genotyping, and health management applications are being performed on a shared station?

Answer

It is extremely important to change the vials each time a sample is removed or loaded onto a probe array. This prevents cross-contamination as well as sample loss. RNase contamination is not an issue with gene expression applications due to the fact that the cRNA sample is fragmented prior to hybridization and is removed prior to array processing on the fluidics station.

Answer Id: E13666

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Product FAQ

For the GeneChip Mouse Expression Set 430, what is a probe set? What do the different suffixes attached to a probe set name mean?

Answer

A probe set is a collection of probes designed to interrogate a given sequence. A probe set name is used to refer to a probe set, which looks like the following:
12345_at or 12345_a_at or 12345_s_at or 12345_x_at
The last three characters (_at, in RED) identify the probe set strand. Probe sets that are designed to detect the anti-sense strand of the gene of interest are annotated with "_at".

There are different types of probe sets that can result from the probe selection process. Most probe sets have an extension of an underscore and a letter to designate the probe set type, except for unique probe sets. These different probe set types are shown in the example above in BLUE. Probes in a gene family probe set (_a set) all cross-hybridize to the same set of sequences that belong to the same gene family (i.e., having same name in the "geneCluster" column). This probe set type is only created if the "geneCluster" column is included in the Instruction File and contains information. Probes in a unique probe set do not cross-hybridize to any other sequences in the design (including any additional pruning sequences provided). Probes in an identical probe set (_s set) all cross-hybridize to the same set of sequences that are used for the design (including any additional pruning sequences if provided). These sequences are not defined as from the same gene family for one the following reasons: the values in the "geneCluster" column are different, or the gene family information is not provided. Probes in a mixed probe set (_x set) contain at least one probe that cross-hybridizes with other sequence(s) used for the design. Cross-hybridizing probes have a cross-hybridization penalty applied to their raw probe scores, and thus, favoring unique probes of the same quality over cross-hybridizing probes.

Answer Id: E14184

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Product FAQ

Can I start using the new 3' IVT Express Kit right away, even in the middle of my experiment?

Answer

We would recommend completing any current project with the same labeling method that you have been using. Although concordance is quite high between the kits, it is best to continue with one labeling method in any experiment. [This answer refers to a product that has been discontinued.]

Answer Id: E14348

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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).

Answer Id: E14090

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Product FAQ

What is the correct fluidics script for the Clariom S (human, mouse and rat) array?

Answer

The Clariom S array is a 400 format, the correct script is FS450_0007.

Answer Id: E14311

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Product FAQ

Which fluidics protocol should I use when processing human, mouse, or rat transcriptome assays?

Answer

FS450_0001 should be used when processing human, mouse, or rat transcriptome assays. Up-to-date fluidics scripts can be obtained from the website.

Answer Id: E14105

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Product FAQ

What are the system requirements to run the Midas software?

Answer

A minimum of 16 GB RAM and 30 GB available disk space is required to perform analysis of Axiom Microbiome cel files.

Answer Id: E14318

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