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GeneChip® Mouse Exon 1.0 ST Array

With approximately four probes per exon and roughly 40 probes per gene, the GeneChip® Mouse 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 1 million 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.


Probe Sets 1.2 million
Exon Clusters ~ 1 million
Supported by Putative Full-Length mRNA 266,220 probe sets
Supported by Ensembl Transcripts 266,791 probe sets
Supported by EST 554,003 probe sets
Supported by Human or Rat mRNA 214,763 probe sets
Supported by Gene Prediction 835,897 probe sets
Probe Selection Region Along the entire length of the transcripts
Probes/Probe Selection Region
Background Subtraction Strategy Median intensity of up to 1,000 background probes with the same GC content
Total Features Per Array >4,500,000
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® Mouse 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® Mouse 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

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Part # Description Details
900817 GeneChip® Mouse Exon 1.0 ST Array Contains 2 arrays
900818 GeneChip® Mouse Exon 1.0 ST Array Contains 6 arrays
900819 GeneChip® Mouse Exon 1.0 ST Array Contains 30 arrays
900831 GeneChip® Mouse Exon 1.0 ST Array Starter Pack Contains 30 arrays and reagents sufficient for 30 reactions

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

Manuals

Expression Analysis Technical Manual, with Specific Protocols for Use with the Hybridization, Wash, and Stain Kit (pdf, 1.70 MB)

Library Files

GeneChip® Medicago Transcriptome Array AGCC Installer

GeneChip® Medicago Transcriptome Array Analysis Files, r1

GeneChip® Medicago Transcriptome Array TAC Analysis Files, r1

Package Inserts

GeneChip® Whole Transcript 49-Format Array (pdf, 168 KB)

Alignment, Annotation, and Sequence Files

Information about using Alignment, Annotation, and Sequence files

NetAffx Alignment Files

MedTA-1_0 BED File, Alfalfa (23 MB, 3/3/16)

MedTA-1_0 BED File, Mt4 (39 MB, 3/10/16)

MedTA-1_0 BED File, R108 (29 MB, 3/3/16)

Current NetAffx Annotation Files

MedTA-1_0 Probeset Annotations, CSV Format, alfalfa, Release 36 (7.2 MB, 3/10/16)

MedTA-1_0 Probeset Annotations, CSV Format, mt4, Release 36 (13 MB, 3/3/16)

MedTA-1_0 Probeset Annotations, CSV Format, r108, Release 36 (7.8 MB, 3/10/16)

MedTA-1_0 Transcript Cluster Annotations, CSV, alfalfa, Release 36 (5.4 MB, 3/10/16)

MedTA-1_0 Transcript Cluster Annotations, CSV, mt4, Release 36 (2.3 MB, 3/10/16)

MedTA-1_0 Transcript Cluster Annotations, CSV, r108, Release 36 (3.5 MB, 3/3/16)

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.

Sequence Files

MedTA-1_0 Probe Sequences, Alfalfa, tabular format (33 MB, 3/10/16)

MedTA-1_0 Probe Sequences, MT4, tabular format (77 MB, 3/10/16)

MedTA-1_0 Probe Sequences, R108, tabular format (42 MB, 3/3/16)

Additional Support

Fluidics Scripts

Probe Set Data in MAGE-ML Format

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