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GeneChip^® Rat Exon 1.0 ST Array

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.

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Tailored GeneChip® Whole Transcript (WT) Assay and Reagents utilizing a random priming method for generating sense targets along the entire length of the transcripts.

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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).

Starter Pack

To ensure optimal results with the GeneChip® Exon Array system, it is highly recommended that new users begin with the Starter Pack. Each Starter Pack contains:

GeneChip® Rat Exon 1.0 ST Array, 30 arrays
GeneChip® WT Sense Target Labeling and Control Reagents, 30 reactions
On-site training including the following arrays and reagents for the training:

GeneChip® Rat Exon 1.0 ST Array, 10 arrays
GeneChip® WT cDNA Synthesis and Amplification Kit, 10 reactions
GeneChip® WT Terminal Labeling Kit, 10 reactions
GeneChip® Sample Cleanup Module, 30 reactions
GeneChip® Eukaryotic Poly-A RNA Control Kit, 100 reactions
GeneChip® Hybridization Control Kit, 30 reactions

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

Windows Media Player | Quicktime

View a two-minute demo on the interpretation of GeneChip® Exon Array data from Biotique's XRAY

Windows Media Player | Quicktime

Data Sheets

Exon Array System (pdf, 464 KB)

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)

Human Exon 1.0 ST Array and WT Sense Target Labeling Assay for Genome-Wide, Exon-Level Expression Analysis (pdf, 624 KB)

Application Notes

Whole-transcript Expression Analysis (pdf, 557 kb)

White Papers

Alternative Transcript Analysis Methods for Exon Arrays v1.1 (pdf, 79 KB)

Exon Array Background Correction v1.0 (pdf, 78 KB)

Exon Probeset Annotations and Transcript Cluster Groupings v1.0 (pdf, 87 KB)

Exon Related Changes FAQ (pdf, 268 KB)

Gene Signal Estimates from Exon Arrays v1.0 (pdf, 428 KB)

Quality Assessment of Exon and Gene 1.0 ST Arrays (pdf, 180 KB)

Publications

Publications and Reference for Affymetrix® GeneChip® Exon and Gene 1.0 ST Arrays (pdf, 74 KB)

Part #	Description	Details
900820	GeneChip® Rat Exon 1.0 ST Array	Contains 2 arrays
900821	GeneChip® Rat Exon 1.0 ST Array	Contains 6 arrays
900822	GeneChip® Rat Exon 1.0 ST Array	Contains 30 arrays
900848	GeneChip® Rat Exon 1.0 ST Array Starter Pack	Contains 30 arrays and reagents sufficient for 30 reactions Additionally, the Starter Pack includes on-site training with the following arrays and reagents; GeneChip® Exon 1.0 ST Array, 10 pack GeneChip® WT cDNA Synthesis and Amplification Kit, 10 rxn GeneChip® WT Terminal Labeling Kit, 10 rxn GeneChip® Sample Cleanup Module, 30 rxn GeneChip® Eukaryotic Poly-A RNA Control Kit, ~100 rxn GeneChip® Hybridization Control Kit, 30 rxn

Related Products

Part #	Description	Details
	Affymetrix® GeneChip® Command Console® Software	Available Via Download
	Affymetrix® Expression Console™ Software	Available Via Download
900652	GeneChip® WT Sense Target Labeling and Control Reagents	Sufficient for 30 reactions
900720	GeneChip® Hybridization, Wash, and Stain Kit	Sufficient for 30 reactions
00-0211	GeneChip® Scanner 3000 7G with Workstation
00-0079	GeneChip® Fluidics Station 450

FAQs

Exon Array Analysis

Exon Array Design

Manuals

Whole Transcript (WT) Sense Target Labeling Assay (pdf, 1.18 MB)

Quick Reference Cards

QC Metrics for Exon and Gene Design Expression Arrays (pdf, 123 KB)

Sample Data

Exon 1.0 ST Array Dataset

Array Comparisons

Comparison Spreadsheets User's Guide (pdf, 82 KB)

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)

Library Files

Rat Exon 1.0 ST Array Analysis (zip, 102 MB)

Rat Exon 1.0 ST Array, GCOS (zip, 3.3 MB)

Unsupported Rat Exon 1.0 ST Array CDF File (zip, 89 MB)

Package Inserts

Rat Exon 1.0 ST Array (pdf, 80 KB)

Alignment, Annotation, and Sequence Files

Information about using Alignment, Annotation, and Sequence files

IGB Annotation Files

Annotations, Rn4, BGN Format

RaEx_1_0-st-v2 Annotations, Rn3/Build 3.1, BGN

Note: The IGB BGN annotation files can be used to load up transcript cluster, probeset, and probe level annotations for the Affymetrix GeneChip® Arrays into IGB. These files allow the user to quickly load a whole chromosome of annotations. For visualizing smaller genic regions the NetAffx IGB links should be used.

Design Time Annotation Files

RaEx-1_0-st-v1 Annotations, Full, Rn3, GFF (222 MB, 2/10/06)

RaEx-1_0-st-v1 Annotations, Probeset, Rn3, CSV (32 MB, 10/6/06)

RaEx-1_0-st-v1 Annotations, Probeset, Rn4, CSV (32 MB, 11/27/06)

RaEx-1_0-st-v1 Design Time Annotations, Full, Rn4, GFF Format (222 MB, 10/9/06)

RaEx-1_0-st-v1 Mappings, TSV (1.5 MB, 3/8/06)

RaEx-1_0-st-v1 Transcript Cluster ID Mappings to Rat 230 (168 KB, 8/28/06)

Note: For gene level analysis you will need to download one of the probeset level annotation zip files (CSV) to get the meta-probeset lists. None of these files contain textual biological annotations such as gene name or GO annotations; textual biological information can be found in the NetAffx Transcript CSV file. The design time Probeset CSV file provides information about the probeset such as genome coordinate and supporting annotation types. This is a subset of information found in the NetAffx Probeset CSV file. The Probeset CSV file is also a subset of the Full GFF files which contain transcript cluster, exon cluster, probeset, and probe level annotations. The GFF files also contain information about the specific annotations supporting each of the probesets. For example, use the Full GFF files for pulling design time information into a local database. The Mappings TSV file contains mappings between other arrays and annotations.

The transcript cluster mapping files provide gene level mappings between 3' IVT probesets and exon array transcript cluster IDs.

Current NetAffx Annotation Files

RaEx-1_0-st-v1 Annotations CSV README (37 KB, 3/11/09)

RaEx-1_0-st-v1 Probeset Annotations, CSV Format (45 MB, 3/16/09)

RaEx-1_0-st-v1 Transcript Cluster Annotations, CSV (14 MB, 3/16/09)

Note: NetAffx annotation files are intended for use in automated analysis. Some are not compatible with all spreadsheet applications. Please use the NetAffx Analysis Center to limit download data to your probe sets of interest. Annotation CSV files for the exon arrays are split into a probe set-level annotation file and a transcript cluster-level annotation file; exon array CSV files are compatible with ExACT.