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Mouse Exon 1.0 ST Array - Support Materials

For more information, please see the product page.

Application Notes

Whole-transcript Expression Analysis (pdf, 557 kb)

Array Comparisons

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

Mouse 430 to Mouse Exon 1.0 ST, Best Match (zip, 1.0 MB)

Mouse 430 to Mouse Exon 1.0 ST, Complex Match (zip, 5.9 MB)

Mouse 430 to Mouse Exon 1.0 ST, Good Match (zip, 1.1 MB)

Mouse 430 to Mouse Exon 1.0 ST, No Match (zip, 515 KB)

Mouse Exon 1.0 ST to Mouse Gene 1.0 ST, Best Match (zip, 599 KB)

Mouse Exon 1.0 ST to Mouse Gene 1.0 ST, Complex Match (zip, 6.7 MB)

Mouse Exon 1.0 ST to Mouse Gene 1.0 ST, Good Match (zip, 820 KB)

Mouse Exon 1.0 ST to Mouse Gene 1.0 ST, No Match (zip, 3 KB)

Data Sheets

Exon Array System (pdf, 3.22MB)-Japanese Version

Exon Array System (pdf, 416 KB)

Frequently Asked Questions

Exon Array Analysis

Exon Array Design

Library Files

Mouse Exon 1.0 ST Array Analysis (zip, 114 MB)

Mouse Exon 1.0 ST Array Probeset, and Meta Probeset Files, core, full, extended and comprehensive mm8 (zip, 14 MB)

Mouse Exon 1.0 ST Array Probeset, and Meta Probeset Files, core, full, extended and comprehensive mm9 (zip, 14 MB)

Mouse Exon 1.0 St Array, GCOS (zip, 2.7 MB)

Unsupported Mouse Exon 1.0 ST Array CDF File (zip, 98 MB)

Manuals

Expression Console™ Software (pdf, 5.57 MB)

Expression Wash, Stain and Scan User Manual for Cartridge Arrays (pdf, 5.41 MB)

Sample Attribute Editor (pdf, 597 KB)

SensationPlus™ FFPE Amplification and WT Labeling Kit (pdf, 391 KB)

Transcriptome Analysis Console (pdf, 9 MB)

WT PLUS Reagent Kit User Manual (pdf, 891 KB)

Publications

Publications and Reference for Affymetrix® GeneChip® Exon and Gene 1.0 ST Arrays (pdf, 289 KB)

Package Inserts

Mouse Exon 1.0 ST Array (pdf, 521 KB)

Quick Reference Cards

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

Sample Data

Exon 1.0 ST Array Dataset

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)

Identifying and Validating Alternative Splicing Events (pdf, 844 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)

Additional Support

Exon Array Announcements

Alignment, Annotation, and Sequence files

Information about using Alignment, Annotation, and Sequence files

IGB Annotation Files

MoEx-1_0-st-v1 Annotations, BGN Format (41 MB, 3/19/08)

MoEx-1_0-st-v1 MoEx_1_0-st-v2 Annotations, Mm5/Build33, BGN (43 MB, 3/1/06)

MoEx-1_0-st-v1 MoEx_1_0-st-v2 Annotations, Mm6/Build 34, BGN (41 MB, 3/1/06)

MoEx-1_0-st-v1 MoEx_1_0-st-v2 Annotations, Mm7/Build 35, BGN (41 MB, 4/19/06)

MoEx-1_0-st-v1 MoEx_1_0-st-v2 Annotations, Mm8/Build 36, BGN (41 MB, 7/14/06)

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.

Current NetAffx Annotation Files

MoEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 33.1 (61 MB, 12/10/12)

MoEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 33.1 (39 MB, 12/10/12)

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 probesets of interest. Annotation CSV files for the exon arrays are split into a probeset level annotation file and a transcript cluster level annotation file; exon array CSV files are compatible with ExACT.

Design Time Annotation Files

MoEx-1_0-st-v1 Annotations, Full, Mm5, GFF (285 MB, 3/6/06)

MoEx-1_0-st-v1 Annotations, Full, Mm6, GFF (285 MB, 3/6/06)

MoEx-1_0-st-v1 Annotations, Full, Mm7, GFF (285 MB, 4/19/06)

MoEx-1_0-st-v1 Annotations, Full, Mm8, GFF (275 MB, 6/21/06)

MoEx-1_0-st-v1 Annotations, Full, Mm9, GFF (278 MB, 3/12/08)

MoEx-1_0-st-v1 Annotations, Probeset, Mm5, CSV (42 MB, 10/6/06)

MoEx-1_0-st-v1 Annotations, Probeset, Mm6, CSV (40 MB, 10/6/06)

MoEx-1_0-st-v1 Annotations, Probeset, Mm7, CSV (42 MB, 10/6/06)

MoEx-1_0-st-v1 Annotations, Probeset, Mm8, CSV (40 MB, 10/6/06)

MoEx-1_0-st-v1 Annotations, Probeset, Mm9, CSV (42 MB, 8/22/08)

MoEx-1_0-st-v1 Mappings, TSV (3.3 MB, 8/18/06)

MoEx-1_0-st-v1 Transcript Cluster ID Mappings to Mouse 430 (296 KB, 8/18/06)

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.

Sequence Files

MoEx-1_0-st-v1 Probe Sequences, FASTA format (154 MB, 3/19/08)

MoEx-1_0-st-v1 Probe Sequences, tabular format (130 MB, 3/19/08)

MoEx-1_0-st-v1 Probeset Sequences FASTA Format (78 MB, 3/19/08)

MoEx-1_0-st-v1 Transcript Cluster Sequences, FASTA format (84 MB, 3/19/08)

Archived NetAffx Annotation Files

MoEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 21 (72 MB, 11/27/06)

MoEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 22 (72 MB, 3/29/07)

MoEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 23 (50 MB, 9/14/07)

MoEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 24 (52 MB, 11/12/07)

MoEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 25 (54 MB, 3/20/08)

MoEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 26 (57 MB, 7/17/08)

MoEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 27 (58 MB, 11/24/08)

MoEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 28 (58 MB, 3/11/09)

MoEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 29 (59 MB, 7/7/09)

MoEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (59 MB, 11/9/09)

MoEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 31 (62 MB, 9/8/10)

MoEx-1_0-st-v1 Probeset Annotations, CSV Format, Release 32 (62 MB, 6/23/11)

MoEx-1_0-st-v1 Probeset Annotations, CSV, Release 20 (64 MB, 7/20/06)

MoEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 20 (15 MB, 7/20/06)

MoEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 21 (18 MB, 6/11/07)

MoEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 22 (21 MB, 6/11/07)

MoEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 23 (15 MB, 9/14/07)

MoEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 24 (11 MB, 11/12/07)

MoEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 25 (12 MB, 3/20/08)

MoEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 26 (16 MB, 7/17/08)

MoEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 27 (16 MB, 11/24/08)

MoEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 28 (16 MB, 3/11/09)

MoEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 29 (18 MB, 7/7/09)

MoEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 30 (18 MB, 11/9/09)

MoEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 31 (20 MB, 9/8/10)

MoEx-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 32 (21 MB, 6/23/11)

Archived Sequence Files

MoEx-1_0-st-v1 Probe Sequences, FASTA (138 MB, 2/21/06)

MoEx-1_0-st-v1 Probe Sequences, FASTA format (137 MB, 11/17/06)

MoEx-1_0-st-v1 Probe Sequences, FASTA format (137 MB, 7/13/07)

MoEx-1_0-st-v1 Probe Sequences, Tabular (128 MB, 2/21/06)

MoEx-1_0-st-v1 Probe Sequences, tabular format (125 MB, 11/17/06)

MoEx-1_0-st-v1 Probe Sequences, tabular format (125 MB, 7/13/07)

MoEx-1_0-st-v1 Probeset Sequences, FASTA (75 MB, 7/19/06)

MoEx-1_0-st-v1 Transcript Cluster Sequences, FASTA format (81 MB, 5/10/07)