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GeneChip^® Rat Gene 1.0 ST Array

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2009年8月より、新しいWTアッセイが始まりました>>

GeneChip® Rat Gene 1.0 ST Array は、転写産物の全長をカバーするアフィメトリクス発現解析アレイファミリーに加わった最新の製品です。27,342の各遺伝子は、その全長にわたって分布する約26個のプローブによってアレイ上に表現されており、3'ベースの発現解析アレイデザインよりも、さらに完全かつ正確な遺伝子発現像を調べることができます。アレイのフォーマットが小さいため、新規のマイクロアレイユーザーにとってはコストパフォーマンスの優れた発現プロファイリングソリューションとなります。センスDNAターゲットは、100ngという少量のトータルRNAから調製されます。

Gene 1.0 ST Arrayは、Whole Transcript（WT）Sense Target Labeling and Control Reagents、Fluidics、スキャニング装置、ならびに基本解析ソフトウェアなどを含む、遺伝子発現解析用の完成されたソリューションの一部です。このアレイには、アノテーションの充実した遺伝子の最新コンテンツが含まれており、シンプルなワークフローを使って、データの解析を行えます。

Gene 1.0 ST Arrayは、Rat Exon 1.0 ST Arrayのプローブの一部を利用しており、十分なアノテーションの付いたコンテンツのみをカバーしています。Exon 1.0 ST Arrayと同様に、「遺伝子レベル」の解析では、異なるエクソンに対応する複数のプローブのデータが、同一の遺伝子から全転写産物に対する発現値にまとめられます。

さらなる情報：

Gene 1.0 ST Arrayによる発現解析のシステム全体に関する詳細はこちら

Rat Gene 1.0 ST Array Coverage

The GeneChip® Rat Gene 1.0 ST Array enables whole-genome, gene-level expression studies for well-characterized genes. It is a single GeneChip®-brand array comprised of more than 700,000 unique 25-mer oligonucleotide features constituting more than 27,000 gene-level probe sets.

The design of the Rat Gene 1.0 ST Array is based primarily on a subset of GeneChip® Rat Exon 1.0 ST Array probes that map to well-supported exons of known genes. Discovery content based solely on Expressed Sequence Tags (ESTs) and RefSeq XMs is not interrogated by the Rat Gene 1.0 ST Array. However, predicted Ensembl EnsGene transcripts are included along with other EnsGene content.

The array design was based on sequences and gene annotations obtained from the following sources and used to group probes into gene-level probe sets. In some cases, these sequences were used to select additional new probes not present on the Rat Exon 1.0 ST Array:

The November 2004 rat genome sequence (UCSC rn4, Baylor HGSC build 3.4)
RefSeq NM (curated and provisional; not predicted) mRNA sequences (10,084 sequences) current to April 3, 2007
GenBank® complete coding sequence mRNAs (12,547 sequences) current to January 25, 2007
Rat Ensembl transcripts current to April 3, 2007 (37,695 transcripts)
Syntenically mapped full-length mRNAs and RefSeq NMs from human (66,206 sequences) and mouse (49,516 sequences)

Data Sheets

Gene 1.0 ST Array System for Human, Mouse and Rat (pdf, 3.07 MB)-Japanese Version

Gene 1.0 ST Array System for Human, Mouse and Rat (pdf, 436 KB)

Technical Notes

Gene 1.0 ST Array Design (pdf, 324 KB)

White Papers

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

Whole Transcript (WT) Sense Target Labeling Assay Performance (pdf, 652 KB)

Publications

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

FAQs

Gene 1.0 ST Array

Manuals

Ambion® WT Expression Kit (pdf, 1.14 MB)

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

WT Terminal Labeling and Hybridization for use with the Ambion® WT Expression Kit (pdf, 447 KB)

Quick Reference Cards

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

Sample Data

Gene 1.0 ST Array Data Set

Array Comparisons

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

Rat 230 to Rat Gene 1.0 ST, Best Match (zip, 272 KB)

Rat 230 to Rat Gene 1.0 ST, Complex Match (zip, 525 KB)

Rat 230 to Rat Gene 1.0 ST, Good Match (zip, 317 KB)

Rat 230 to Rat Gene 1.0 ST, No Match (zip, 39 KB)

Rat Exon 1.0 ST to Rat Gene 1.0 ST, Best Match (zip 865 KB)

Rat Exon 1.0 ST to Rat Gene 1.0 ST, Complex Match (zip 4.9 MB)

Rat Exon 1.0 ST to Rat Gene 1.0 ST, Good Match (zip 1.0 MB)

Rat Exon 1.0 ST to Rat Gene 1.0 ST, No Match (zip 4 KB)

Library Files

Probe BED File

Rat Gene 1.0 ST Array, Analysis (zip, 19 MB)

Rat Gene 1.0 ST Array, GCOS (2.4 MB)

Unsupported Rat Gene 1.0 ST Array CDF Files (zip, 12 MB)

Package Inserts

Rat Gene 1.0 ST Array (pdf, 152 KB)

Alignment, Annotation, and Sequence Files

Information about using Alignment, Annotation, and Sequence files

NetAffx Alignment Files

RaGene-1_0-st-v1 BED File (13 MB, 1/9/09)

Design Time Annotation Files

RaGene-1_0-st-v1 Design Time Annotations, Full, GFF Format (22 MB, 8/31/07)

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.

Current NetAffx Annotation Files

RaGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 32 (6.1 MB, 6/23/11)

RaGene-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 32 (8.5 MB, 6/23/11)

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

RaGene-1_0-st-v1 Probe Sequences, FASTA format (24 MB, 9/5/07)

RaGene-1_0-st-v1 Probe Sequences, tabular format (20 MB, 9/5/07)

RaGene-1_0-st-v1 Transcript Cluster Sequences, FASTA format (14 MB, 9/5/07)

Archived NetAffx Annotation Files

RaGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 27 (5.9 MB, 2/12/09)

RaGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 27 (5.9 MB, 2/18/09)

RaGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 27 (5.9 MB, 1/16/09)

RaGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 28 (5.9 MB, 3/11/09)

RaGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 29 (6.0 MB, 7/23/09)

RaGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (6.0 MB, 12/8/09)

RaGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (6.0 MB, 11/9/09)

RaGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 31 (6.1 MB, 8/27/10)

RaGene-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 23 (7.4 MB, 9/17/07)

RaGene-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 24 (3.8 MB, 11/12/07)

RaGene-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 25 (4.6 MB, 3/20/08)

RaGene-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 26 (6.2 MB, 7/17/08)

RaGene-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 27 (6.4 MB, 11/24/08)

RaGene-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 28 (6.4 MB, 3/11/09)

RaGene-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 29 (7.1 MB, 7/23/09)

RaGene-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 30 (7.1 MB, 12/8/09)

RaGene-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 30 (7.1 MB, 11/9/09)

RaGene-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 31 (8.2 MB, 8/27/10)