GeneChip® Rat Gene ST Arrays
The whole-transcript coverage of these arrays provide the most accurate, sensitive, and comprehensive measurement of protein coding and non-coding RNA transcripts.
Comprehensive design
Affymetrix understands that rats are an important model organism commonly used for studying human disease. In order to keep your experiments relevant to the understanding of the transcriptome, Affymetrix has designed an array based on the most recent genome content for generating genome-wide expression profiles.
The GeneChip® Gene ST family of arrays offers a unique feature not available in other microarrays. Unlike traditional array designs that rely on a probe(s) designed to the first exon of the gene's 3' end, the hundreds of thousands of probes on each GeneChip Gene ST Array are designed to every exon of every transcript represented on the array.
The high transcript coverage (median of 22 probes per gene) yields accurate detection for genome-wide transcript expression changes. These arrays provide higher resolution and accuracy than many of the classical 3'-biased microarray solutions available. The whole-transcript analysis approach enables researchers to detect multiple transcript isoforms from a given gene, including those that could be missed using a 3'-biased expression design, such as splice variants, non-polyadenylated transcripts, transcripts with alternative polyadenylation sites, and truncated transcripts.
Key benefits
- Whole-transcript analysis enables the capture of transcript isoforms you may miss with 3'-biased expression designs
- Comprehensive transcriptome coverage provides the best opportunity to discover interesting biology:
- >27,000 protein coding transcripts
- >24,000 Entrez genes
- Measure alternative splicing events/transcript variants with probes designed to maximize coverage of exons
- Reproducible: Signal correlation coefficient ≥0.99
Content profile
Since the design of GeneChip® Rat Gene 1.0 ST Array, there has a substantial increase in the structural and functional understanding of the Rat genome. In order to provide the research community with a tool that can measure the differential expression of this exciting class of RNA transcripts, Affymetrix designed GeneChip® Rat Gene 2.0 ST Array.
| Transcript coverage of the array1 | Rat Gene 1.0 ST Array | Rat Gene 2.0 ST Array |
|---|---|---|
| Total RefSeq transcripts covered | 17,061 | 28,407 |
| NM – RefSeq coding transcript, well-established annotation | 16,054 | 16,771 |
| NR – RefSeq non-coding transcript, well-established annotation | 293 | 442 |
| XM – RefSeq coding transcript, provisional annotation | 642 | 10,376 |
| XR – RefSeq non-coding transcript, provisional annotation | 72 | 818 |
| RefSeq (Entrez) Gene count | 16,557 | 23,586 |
| 1 Transcript coverage and gene count derived from RefSeq download as of February 2012. | ||
| Data sources used to design the array | Rat Gene 1.0 ST Array | Rat Gene 2.0 ST Array |
|---|---|---|
| RefSeq | 36 | 51 |
| Ensembl | 41 | 65 |
| GenBank | Nov. 2006 | - |
| UCSC | RN4 | - |
| Baylor College of Medicine Human Genome Sequencing Center & Rat Genome Sequencing Consortium (RGSC) | RN3.4 | - |
"For Research Use Only. Not for use in diagnostic procedures."
Required Products
Related Products
| GeneChip® Rat Exon ST Array |
| Affymetrix® Rat Gene ST Array Strips |
| Affymetrix® Rat Gene ST Array Plates |