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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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