GeneChip Rat Gene 1.0 ST Array

The GeneChip® Rat Gene 1.0 ST Array is the latest product in the family of Affymetrix expression arrays offering whole-transcript coverage. Each of the 27,342 genes is represented on the array by approximately 26 probes spread across the full length of the gene, providing a more complete and more accurate picture of gene expression than 3’-based expression array designs. The small format of the array makes it a cost-effective expression profiling solution for new microarray users. Sense DNA targets are generated from as little as 100ng of total RNA.

The Gene 1.0 ST Array is part of a complete solution for gene expression analysis that includes Whole Transcript (WT) Sense Target Labeling and Control Reagents, fluidics and scanning instrumentation and basic analysis software. The array contains the most up-to-date content of well-annotated genes, and data is analyzed using a simple workflow.

The Gene 1.0 ST Array uses a subset of probes from the Rat Exon 1.0 ST Array and covers only well-annotated content. Like the Exon 1.0 ST Array, “gene-level” analysis of multiple probes on different exons is summarized into an expression value representing all transcripts from the same gene.

Rat Gene 1.0 ST Array Coverage

The GeneChip® Rat Gene 1.0 ST Array enables whole-genome, gene-level expression studies for well-characterized genes. It is a single GeneChip®-brand array comprised of more than 700,000 unique 25-mer oligonucleotide features constituting more than 27,000 gene-level probe sets.

The design of the Rat Gene 1.0 ST Array is based primarily on a subset of GeneChip® Rat Exon 1.0 ST Array probes that map to well-supported exons of known genes. Discovery content based solely on Expressed Sequence Tags (ESTs) and RefSeq XMs is not interrogated by the Rat Gene 1.0 ST Array. However, predicted Ensembl EnsGene transcripts are included along with other EnsGene content.

The array design was based on sequences and gene annotations obtained from the following sources and used to group probes into gene-level probe sets. In some cases, these sequences were used to select additional new probes not present on the Rat Exon 1.0 ST Array:

• The November 2004 rat genome sequence (UCSC rn4, Baylor HGSC build 3.4)
  
• RefSeq NM (curated and provisional; not predicted) mRNA sequences (10,084 sequences) current to April 3, 2007
  
• GenBank® complete coding sequence mRNAs (12,547 sequences) current to January 25, 2007
  
• Rat Ensembl transcripts current to April 3, 2007 (37,695 transcripts)
  
• Syntenically mapped full-length mRNAs and RefSeq NMs from human (66,206 sequences) and mouse (49,516 sequences)

Complete Reagents, Software and Instrumentation
Solution for Optimal Array Performance

For convenience and complete support, the Gene 1.0 ST Array is provided as part of a comprehensive solution that includes Affymetrix reagents and instrumentation:

• GeneChip® WT Sense Target Labeling and Control Reagents. For detailed information on the procedure of the assay and performance information, please refer to the WT Sense Target Labeling Assay Manual
  
• GeneChip® Fluidics Station 450 for complete walk-away array processing to obtain the highest levels of reproducibility
  
• GeneChip® Scanner 3000 7G with the optional Autoloader for array image acquisition

Affymetrix offers several tools to help you in your data analysis, including Affymetrix® Expression Console™ software, the NetAffx™ Analysis Center, and the Integrated Genome Browser (IGB).

Expression Console software is an easy-to-use application that enables probe set summarization as well as preliminary data quality evaluation. A simple workflow enables the user to quickly analyze the data (see figure). The resulting data can be further analyzed using software applications from Affymetrix GeneChip®-compatible™ software providers.

The NetAffx Analysis Center, with regularly updated biological and functional annotations of probe sets, is the most comprehensive resource for array annotations and probe sequence information. Flexible query tools and external links allow researchers to drill down into genes and annotations of interest. This resource makes it easy to interpret microarray results and quickly design downstream studies.

Workflow

Researchers can also use IGB to visualize results in a genomic context. Genomic annotations including RefSeq sequences, SNPs and genomic locations from various sources can be viewed alongside microarray gene expression signal data.

The Gene 1.0 ST Array data analysis workflow is similar to the workflow for 3’ gene expression analysis, utilizing Expression Console 1.1, third-party GeneChip®-compatible™ software and annotation tools in the NetAffx™ Analysis Center and IGB.

For research use only. Not for use in diagnostic procedures.