GeneChip® Rat Exon ST Array
GeneChip® Rat Exon ST Array offers new insight and powerful key information for researchers.
With approximately four probes per exon and roughly 40 probes per gene, the GeneChip® Rat Exon 1.0 ST Array enables two complementary levels of analysis—gene expression and alternative splicing.
Multiple probes per exon enable "exon-level" analysis and allow you to distinguish between different isoforms of a gene. This exon-level analysis on a whole-genome scale opens the door to detecting specific alterations in exon usage that may play a central role in disease mechanism and etiology.
The second level is "gene-level" expression analysis, in which multiple probes on different exons are summarized into an expression value of all transcripts from the same gene.
Exon arrays provide the most comprehensive coverage of the genome, including empirically supported and predicted transcribed sequences, enabling the discovery of previously unidentified novel events.
Array Features
- Highest resolution expression analysis, interrogating over 850,000 exon clusters within the known and predicted transcribed regions of the entire genome.
- Tailored GeneChip® Whole Transcript (WT) Assay and Reagents utilizing a random priming method for generating sense targets along the entire length of the transcripts.
- Flexible data analysis solutions and comprehensive annotation, giving you the opportunity to explore and dissect the data in various user-defined workflows.
Design Statistics Summary
| Probe Sets | ~ 1 million |
| Exon Clusters | 850,000 |
| Supported by Putative Full-Length mRNA | 92,038 probe sets |
| Supported by Ensembl Transcripts | 195,943 probe sets |
| Supported by EST | 211,451 probe sets |
| Supported by Human or Rat mRNA | 272,061 probe sets |
| Supported by Gene Prediction | 875,666 probe sets |
| Probe Selection Region | Along the entire length of the transcripts |
| Probes/Probe Selection Region | 4¹ |
| Background Subtraction Strategy | Median intensity of up to 1,000 background probes with the same GC content |
| Total Features Per Array | ~ 4,000,000 |
| Interrogated Strand | Sense² |
| ¹ About 10 percent of the exon probe sets have fewer than four probes due to the probe selection region length and sequence constraints. ² The probes tiled on the array are designed in the anti-sense orientation, requiring sense-strand labeled targets to be hybridized to the array. By convention, the array is called ST array representing the necessity of using sense targets (the labeled samples to be hybridized to the array). | |
New XRAY demos for exon expression analysis
- View a two-minute demo on a typical workflow using Biotique's XRAY for the analysis of GeneChip® Exon Arrays
- View a two-minute demo on the interpretation of GeneChip® Exon Array data from Biotique's XRAY
Windows Media Player | Quicktime
For research use only. Not for use in diagnostic procedures.
Application Notes
Whole-transcript Expression Analysis (pdf, 557 kb)
Comparison Sheets / Array Comparisons
Rat 230 to Rat Exon 1.0 ST, Best Match (zip, 570 KB)
Rat 230 to Rat Exon 1.0 ST, Complex Match (zip, 1.6 MB)
Rat 230 to Rat Exon 1.0 ST, Good Match (zip, 606 KB)
Rat 230 to Rat Exon 1.0 ST, No Match (zip, 720 KB)
Comparison Spreadsheets User's Guide (pdf, 82 KB)
Data Sheets
Exon Array System (pdf, 416 KB)
FAQs
Library Files
Rat Exon 1.0 ST Array Analysis (zip, 102 MB)
Unsupported Rat Exon 1.0 ST Array CDF File (zip, 89 MB)
Rat Exon 1.0 ST Array, GCOS (zip, 3.3 MB)
Manuals
Ambion® WT Expression Kit (pdf, 1.13 MB)
WT Terminal Labeling and Hybridization for use with the Ambion® WT Expression Kit (pdf, 425 KB)
Expression Wash, Stain and Scan User Manual for Cartridge Arrays (pdf, 5.41 MB)
Package Inserts
Rat Exon 1.0 ST Array (pdf, 80 KB)
Publications
Publications and Reference for Affymetrix GeneChip Exon and Gene 1.0 ST Arrays (pdf, 289 KB)
Quick Reference Cards
QC Metrics for Exon and Gene Design Expression Arrays (pdf, 123 KB)
Sample Data
Technical Notes
Array Design for the Human Exon 1.0 ST Array (pdf, 348 KB)
Guide to Probe Logarithmic Intensity Error (PLIER) Estimation (pdf, 294 KB)
White Papers
Exon Related Changes FAQ (pdf, 268 KB)
Quality Assessment of Exon and Gene 1.0 ST Arrays (pdf, 180 KB)
Gene Signal Estimates from Exon Arrays v1.0 (pdf, 428 KB)
Exon Probeset Annotations and Transcript Cluster Groupings v1.0 (pdf, 87 KB)
Alternative Transcript Analysis Methods for Exon Arrays v1.1 (pdf, 79 KB)
Exon Array Background Correction v1.0 (pdf, 78 KB)
Other
Design Time Annotation Files
RaEx-1_0-st-v1 Transcript Cluster ID Mappings to Rat 230 (172 KB 08/28/06)
RaEx-1_0-st-v1 Annotations, Full, Rn3, GFF (233 MB 02/10/06)
RaEx-1_0-st-v1 Mappings, TSV (2 MB 03/08/06)
RaEx-1_0-st-v1 Annotations, Probeset, Rn3, CSV (34 MB 10/06/06)
RaEx-1_0-st-v1 Design Time Annotations, Full, Rn4, GFF Format (233 MB 10/09/06)
RaEx-1_0-st-v1 Annotations, Probeset, Rn4, CSV (34 MB 11/27/06)
IGB Annotation Files
RaEx-1_0-st-v1 RaEx_1_0-st-v2 Annotations, Rn3/Build 3.1, BGN (39 MB 02/27/06)
RaEx-1_0-st-v1 Annotations, Rn4, BGN Format (39 MB 11/17/06)
NetAffx Annotation Files
RaEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 32 (50 MB 06/23/11)
RaEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 31 (19 MB 08/27/10)
RaEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 31 (50 MB 08/27/10)
RaEx-1_0-st-v1 Annotations CSV README, Release 30 (39 KB 11/09/09)
RaEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (48 MB 11/09/09)
RaEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 30 (17 MB 11/09/09)
RaEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 32 (19 MB 06/23/11)
Sequence Files
RaEx-1_0-st-v1 Sequence Files README (12 KB 03/19/08)
RaEx-1_0-st-v1 Probe Sequences, FASTA format (139 MB 03/19/08)
RaEx-1_0-st-v1 Probe Sequences, tabular format (118 MB 03/19/08)
RaEx-1_0-st-v1 Probeset Sequences FASTA Format (61 MB 03/19/08)
RaEx-1_0-st-v1 Transcript Cluster Sequences, FASTA format (60 MB 03/19/08)
Archived NetAffx Annotation Files
RaEx-1_0-st-v1 Annotations README, Release 20 (29 KB 07/20/06)
RaEx-1_0-st-v1 Probeset Annotations, CSV, Release 20 (52 MB 07/20/06)
RaEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 20 (14 MB 07/20/06)
RaEx-1_0-st-v1 Annotations CSV README, Release 21 (32 KB 11/27/06)
RaEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 21 (56 MB 11/27/06)
RaEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 21 (17 MB 06/11/07)
RaEx-1_0-st-v1 Annotations CSV README, Release 22 (44 KB 03/28/07)
RaEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 22 (56 MB 03/29/07)
RaEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 22 (17 MB 06/11/07)
RaEx-1_0-st-v1 Annotations CSV README, Release 23 (37 KB 07/13/07)
RaEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 23 (45 MB 09/14/07)
RaEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 23 (14 MB 09/14/07)
RaEx-1_0-st-v1 Annotations CSV README, Release 24 (37 KB 11/12/07)
RaEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 24 (45 MB 11/12/07)
RaEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 24 (12 MB 11/12/07)
RaEx-1_0-st-v1 Annotations CSV README, Release 25 (37 KB 03/19/08)
RaEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 25 (46 MB 03/20/08)
RaEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 25 (13 MB 03/20/08)
RaEx-1_0-st-v1 Annotations CSV README, Release 26 (39 KB 07/08/08)
RaEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 26 (48 MB 07/17/08)
RaEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 26 (15 MB 07/17/08)
RaEx-1_0-st-v1 Annotations CSV README, Release 27 (39 KB 11/24/08)
RaEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 27 (48 MB 11/24/08)
RaEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 27 (15 MB 11/24/08)
RaEx-1_0-st-v1 Annotations CSV README, Release 28 (39 KB 03/11/09)
RaEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 28 (48 MB 03/16/09)
RaEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 28 (15 MB 03/16/09)
RaEx-1_0-st-v1 Annotations CSV README, Release 29 (39 KB 06/25/09)
RaEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 29 (49 MB 07/07/09)
RaEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 29 (16 MB 07/07/09)
Archived Sequence Files
RaEx-1_0-st-v1 Probe Sequences, FASTA (60 MB 02/21/06)
RaEx-1_0-st-v1 Probe Sequences, FASTA (124 MB 02/21/06)
RaEx-1_0-st-v1 Probe Sequences, Tabular (115 MB 02/21/06)
RaEx-1_0-st-v1 Probe Sequences, FASTA format (129 MB 11/17/06)
RaEx-1_0-st-v1 Probe Sequences, tabular format (117 MB 11/17/06)
RaEx-1_0-st-v1 Probeset Sequences FASTA Format (60 MB 11/17/06)
RaEx-1_0-st-v1 Sequence Files README (12 KB 05/10/07)
RaEx-1_0-st-v1 Transcript Cluster Sequences, FASTA format (60 MB 05/10/07)
RaEx-1_0-st-v1 Sequence Files README (11 KB 07/13/07)
RaEx-1_0-st-v1 Probe Sequences, FASTA format (129 MB 07/13/07)
RaEx-1_0-st-v1 Probe Sequences, tabular format (117 MB 07/13/07)
Required Products
Related Products
| GeneChip® Mouse Gene ST Arrays |
| Affymetrix® Mouse Gene ST Array Plates |