GeneChip™ Rat Genome 230 2.0 Array, 30 arrays - FAQs

View additional product information for GeneChip™ Rat Genome 230 2.0 Array - FAQs (900507, 900506, 900505)

13 product FAQs found

What reagent kit should I use with my array?

Please refer to the Microarray Reagent Guide for Arrays and Expression Kits to match the correct reagents your array.

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How are transcript IDs assigned for WT arrays if a gene has multiple transcript IDs?

The first assigned mRNA/gene that is listed in the annotation file for a given probe set or transcript cluster is considered the "best" assignment based on data source quality ranking and assignment scoring system. To get a single best mRNA/gene assignment you can simply take the first one in the list in the annotation file.

Sometimes, there might be multiple best hits between transcript clusters (or probe set) and a mRNA/gene, with identical score and data source quality. In that case, the transcript assignments are ranked based on their descriptions (e.g., title from the GenBank record).

For transcript clusters that detect genes that are alternatively spliced, the different spliced forms will be ranked by length with the longest ones listed first.

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Does the GeneChip miRNA 3.1 Array Strip require a different hyb/wash/stain kit than the GeneChip 3' IVT arrays and GeneChip ST array strips?

The hyb/wash/stain kit for the GeneChip miRNA 3.1 Array Strips is different than that for the 3' IVT arrays and GeneChip ST array strips. Additional wash A steps have been added to ensure adequate washing after the array strips have been stained.

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What do the suffixes mean at the end of each probeset in GeneChip 3' IVT arrays?

The probe set names never change, but they can give you an idea of what was known about the sequence at the time of design.
_at: All probes hit one known transcript.
_a: All probes in the set hit alternate transcripts from the same gene.
_s: All probes in the set hit transcripts from different genes.
_x: Some probes hit transcripts from different genes.

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Can I store my GeneChip 3' IVT Array after hybridization?

Yes, but we recommend storing your GeneChip 3' IVT Array after hybridization and prior to the fluidics step, for no longer than 3 hours at 4 degrees C. Please remove the hybridization cocktail and fill with wash A before storing.

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What is the probe orientation on the IVT Expression chips?

The probes on the 3' IVT platform are in the sense orientation.

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Is it possible to compare different array types (e.g., Rat 230A and Rat 230 2.0) in GeneChip Command Console (GCC)?

GeneChip Command Console cannot generate a comparison analysis between different array types.

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How long does the scan of a Rat 230 2.0 Array take?

Scanning a single Rat 230 2.0 array takes approximately 9 minutes. This is about 25% less time than is required to scan the Rat 230A and Rat 230B arrays combined.

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How much memory is needed to store the data from a single Rat 230 2.0 Array?

A single Rat 230 2.0 array generates approximately 92 MB of data.

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Where can I find the high-resolution scanning patch for the Rat 230 2.0 Array?

Please contact Technical Support to obtain the high-resolutiion scanning patch.

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Do I have to apply the high-resolution scanning patch for the Rat 230 2.0 Array?

Below are a list of circumstances and clarification on if the high-resolution scanning patch needs to be applied. Keep in mind that the high-resolution scanning patch must only be applied on top of GCOS, not AGCC software.

a. GeneChip Scanner 3000 (serial numbers 502xxxxx): The instrument service engineer has applied the high-resolution scanning patch to the computer that is controlling the GeneChip Scanner 3000 at installation, but not to the workstations or servers (see c and d below).

b. GeneChip Scanner 3000 (serial numbers 501xxxxx): The instrument service engineer will apply the high-resolution scanning patch to the computer that is controlling the GeneChip Scanner 3000 at the time of the upgrade, but not to the workstations or servers (see c and d below).

c. Analysis workstations and clients: You must apply the high-resolution scanning patch. d. Server upgrade: Your database administrator or an Affymetrix Software Support Engineer needs to apply the high-resolution scanning patch in coordination with the upgrade of server to GCOS.

e. Installation of library files post scanner installation or upgrade: The high-resolution scanning patch must be reapplied following the installation of library files for arrays that precede the Rat 230 2.0 Array. The Rat 230 2.0 array and library files are high-resolution-scanning ready. The error message "cannot read the parameters for probe array type from the database" appears when one tries to scan an array on a GeneChip Scanner 3000 high-resolution scanner but the high-resolution scanning patch has not been applied

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How do I know if my GeneChip Scanner 3000 has been enabled for high-resolution scanning that is needed for the Rat 230 2.0 Array?

a. GeneChip Scanner 3000s that were shipped after September 15, 2003 with serial number 502xxx are enabled for high-resolution scanning.

b. GeneChip Scanner 3000s that were shipped prior to September 15, 2003 with serial number 501xxx that have had the GeneChip Scanner 3000 High-Resolution Update installed by an instrument service engineer are enabled for high-resolution scanning. A sticker is applied to the rear of the scanner to indicate that the upgrade has been performed.

c. Contact technical support at techsupport@thermofisher.com to inquire about a scanner upgrade.

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What are the instrumentation and software requirements for the Rat Genome 230 2.0 Array?

For array hybridization, washing, staining and scanning, the following instrumentation is required:

-GeneChip Scanner 3000 7G
-Fluidics Station 450
-Hybridization Oven 640 or Hybridization Oven 645
br/> Data acquisition and analysis of Mouse 430 2.0 Arrays requires the following software:

-GeneChip Command Console Software
-Expression Console Software


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