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GeneChip Sugar Cane Genome Array

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Data Sheet

GeneChip Sugar Cane Genome Array

The GeneChip Sugar Cane Genome Array is designed specifically to monitor gene expression in sugar cane (Saccharum officinarum). The array consists of over 8,200 probe sets to interrogate approximately 7,500 sugar cane transcripts including 4,447 sugar cane UniGene clusters. The Sugar Cane Genome Array is particularly useful for agriculture researchers studying gene expression in the sugar cane plant. The Sugar Cane Genome Array was created in collaboration with leading sugar cane researchers through the GeneChip Consortia Program and was designed based on content from Saccharum officinarum UniGene Build 5 from August 27th, 2004 and GenBank mRNAs up to November 2, 2004.

Sugar cane is an important food crop worldwide. In the EU and many other countries such as Brazil, Australia, Thailand, and India, sugar cane is one of the top export crops. Many research programs utilize genomic approaches to aid selective breeding programs by identifying the underlying genetic mechanisms that are important for high-yield resistance to diseases and insects, and sense environmental factors that determine the productive growing areas for sugar cane. The GeneChip Sugar Cane Genome Array provides a tool that enables researchers to elucidate these complex genetic traits and many others in the Sugar Cane plant to determine how crop production can be improved.

contains 11 probe pairs per probe set. Content for the array utilizes content from Saccharum officinarum UniGene Build 5 (August 27th, 2004) and GenBank mRNAs up to November 2, 2004. The array contains 8,236 S. officinarum probe sets to monitor gene expression for approximately 6,024 distinct S. officinarum genes (including both Unigene and nonUnigene gene clusters).

Instrument Software Requirements

GeneChip Scanner 3000, enabled for High-Resolution Scanning* GeneChip Operating Software (GCOS)

v1.1.1, which contains the HighResolution Scanning Update

*GeneChip Scanner 3000 High-Resolution Update is standard on all instruments shipped starting in September 2003 with serial number series 502. Previous versions (serial number series 501) will require the 00-0110 GeneChip Scanner 3000 HighResolution Update to be installed.

Array Profile
The GeneChip Sugar Cane Genome Array is a 169-format, 11-micron array design, and it

Critical Specifications
Probe Sets: Transcripts: UniGene Clusters: Number of arrays in set Array format Feature size Oligonucleotide probe length Probe pairs/sequence Hybridization controls: Poly-A controls: Housekeeping/Control genes: Detection sensitivity 8,224 sugar cane sets + 12 sugar cane control sets 7,503 sugar cane transcripts + 3 sugar cane control transcripts 4,447 sugar cane UniGene clusters One 169 11 m 25-mer 11 bioB, bioC, bioD from E. coli and cre from P1 Bacteriophage dap, lys, phe, thr, trp from B. subtilis Actin, ef1a, and GAPDH. 1:100,000*

* As measured by detection in comparative analysis between a complex target containing spiked control transcriptions and a complex target with no spikes.

Supporting Products
Part Number 900493 Product Name One-Cycle Target Labeling and Control Reagents1 Description Sufficient for 30 reactions. Contains: IVT Labeling Kit One-Cycle cDNA Synthesis Kit Sample Cleanup Module Poly-A RNA Control Kit Hybridization Controls Sufficient for 30 reactions. Contains: IVT Labeling Kit Two-Cycle cDNA Synthesis Kit Sample Cleanup Module Poly-A RNA Control Kit Hybridization Controls

Ordering Information GeneChip Sugar Cane Genome Array

GeneChip Sugar Cane Genome Array


Two-Cycle Target Labeling and Control Reagents1,2

900626 Contains 2 Arrays 900627 Contains 6 Arrays 900628 Contains 30 Arrays

To Order North America 888-DNA-CHIP 888-362-2447 Europe +44 (0) 1628 552550 Japan +81-(0)3-5730-8200

1Individual Kit components may be ordered separately. 2For the intermediate IVT step with unlabeled nucleotides, please order the MEGAscript T7 Kit directly

from Ambion.
Affymetrix products can be purchased directly from Affymetrix in the United States, many European countries, and many Asian countries. For all other territories, please view a list of our distribution partners, which can be located at:

AFFYMETRIX, INC. 3380 Central Expressway Santa Clara, CA 95051 USA Tel: 1-888-DNA-CHIP (1-888-362-2447) Fax: 1-408-731-5441

AFFYMETRIX UK Ltd Voyager, Mercury Park, Wycombe Lane, Wooburn Green, High Wycombe HP10 0HH United Kingdom Tel: +44 (0) 1628 552550 Fax: +44 (0) 1628 552585

AFFYMETRIX JAPAN K.K. Mita NN Bldg., 16 F 4-1-23 Shiba, Minato-ku, Tokyo 108-0014 Japan Tel: +81-(0)3-5730-8200 Fax: +81-(0)3-5730-8201 Please visit our web site for international distributor contact information. For research use only. Not for use in diagnostic procedures.
Part No. 701924 Rev. 1 2005 Affymetrix, Inc. All rights reserved. Affymetrix,GeneChip, , , , HuSNP, Jaguar, EASI, MicroDB, GenFlex, CustomExpress, CustomSeq, NetAffx, Tools to take you as far as your vision, and The Way Ahead are trademarks owned or used by Affymetrix, Inc. Array products may be covered by one or more of the following patents and/or sold under license from Oxford Gene Technology: U.S. Patent Nos. 5,445,934; 5,700,637; 5,744,305; 5,945,334; 6,054,270; 6,140,044; 6,261,776; 6,291,183; 6,346,413; 6,399,365; 6,420,169; 6,551,817; 6,610,482; 6,733,977; and EP 619 321; 373 203 and other U.S. or foreign patents.