Genechip Arabidopsis Tiling 1.0R Array

ARRAYS Critical Speciﬁ cations Feature Size 5 µm Tiling Resolution 35 base pair Hybridization Controls bioB, bioC, bioD, cre Tiling mRNA controls B. subtilis: dap, lys, phe, thr A. thaliana: CAB, RCA, RBCL, LTP4, LTP6, XCP2, RCP1, NAC1, TIM, PRKASE Array Format 49 Fluidics Protocol Fluidics Station 450: FS450_0001 Fluidics Station 400: EukGE-WS2v5, and manually add Array Holding Buffer to the cartridge prior to scanning Hybridization Volume 200 µL. The total ﬁ ll volume of the cartridge is 250 µL. Library Files At35b_MR_v04 At35b_MR_v04-2_TIGRv5.bpmap GeneChip® Arabidopsis Tiling 1.0R Array RECOMMENDED ANALYSIS SOFTWARE 1. Affymetrix® Tiling Array Software (TAS) For studying protein/DNA interactions or identifying novel tran- 2. Integrated Genome Browser scripts in Arabidopsis thaliana. TAS and the Integrated Genome Browser are available for download from www.affymetrix.com

ACCESSORY FILES Fluidics The ﬂ uidics scripts can be downloaded from the Affymetrix web site. Addi- tional information, including lists of steps in the ﬂ uidics protocol, can be found in the Affymetrix® Chromatin Immunoprecipitation Assay Protocol oorr tthehe GeneChip® WT Double-Stranded Target Assay Manual.

Library Files Library fi les contain information about the probe array design layout and other characteristics, probe use and content, and scanning and analysis pa- INTENDED USE rameters. Tiling arrays are accompanied by .bpmap fi les which associate each The GeneChip® Arabidopsis Tiling 1.0R Array is designed for identifying probe on the array with the genomic location. These fi les are unique for each novel transcripts or mapping sites of protein/DNA interaction in chromatin probe array type. The library fi les can be downloaded from the following immunoprecipitation (ChIP) experiments. The Arabidopsis Tiling 1.0R Array URL: www.affymetrix.com/support/technical/libraryfi lesmain.affx is a single array comprised of over 3.2 million perfect match/mismatch probe pairs tiled through the complete non-repetitive Arabidopsis thaliana genome. Sequences used in the design of the Arabidopsis Tiling 1.0R Array were ORDERING INFORMATION selected from NCBI Arabidopsis genome assembly (Version 5). Mitochondrial and chloroplast sequences were selected from NCBI (Accession numbers NC_ P/N Product Name Description 001284 and NC_000932). Huaming Chen and Joe Ecker of the Salk Institute ARRAYS for Biological Studies contributed to the array design by collecting sequences 900594 GeneChip® Arabidopsis Tiling 1.0R Array 6 Arrays and developing a method for removing repetitive sequences. In this method, identical regions were removed, and similar sequences were retained. At least SUPPORTING PRODUCTS one copy of repetitive sequences was retained in the design. 900813 GeneChip® WT Double-Stranded cDNA Suffi cient for Oligonucleotide probes are synthesized in situ complementary to each cor- Synthesis Kit1 30 Reactions responding sequence. Probes are tiled at an average resolution of 35 base pairs, 900301 Control Oligo B2, 3nM Suffi cient for as measured from the central position of adjacent 25-mer oligos, leaving a gap 30 Reactions of approximately 10 base pairs between probes. 900812 GeneChip® WT Double-Stranded DNA Suffi cient for GeneChip probe arrays are for research use only and not intended for use Terminal Labeling Kit2 30 Reactions ® in diagnosis of disease. Refer to the Affymetrix Chromatin Immunoprecipitation 900720 GeneChip® Hybridization, Wash, and Stain Suffi cient for Assay Protocol oror thethe GeneChip® WT Double-Stranded Target Assay Manual forfor Kit 30 Reactions procedures regarding target preparation, target hybridization, fl uidics station 1 For use with the GeneChip® WT Double-Stranded Target Assay setup, probe array scanning, and data analysis. 2 For use with both the Affymetrix® Chromatin Immunoprecipitation Assay and the GeneChip® WT Double-Stranded Target Assay

® INSTRUMENTATION AND SOFTWARE REQUIRED Affymetrix products can be purchased directly from Affymetrix in the 1. GeneChip® Scanner 3000 7G United States, many European countries, and many Asian countries. For all 2. GeneChip® Operating Software (GCOS) version 1.3 or higher other territories, please view a list of our distribution partners, which can be 3. GeneChip® Fluidics Station 400 or higher located at: www.affymetrix.com/site/contact/index.affx

GeneChip® Arabidopsis Tiling 1.0R Array PRECAUTIONS CONTACT INFORMATION 1. GENECHIP PROBE ARRAYS ARE FOR RESEARCH USE ONLY; NOT Affymetrix, Inc. FOR DIAGNOSTIC PROCEDURES. 3420 Central Expressway 2. Avoid microbial contamination, which may cause erroneous results. Santa Clara, CA 95051 USA 3. WARNING: All biological specimens and materials with which they E-mail: [email protected] come into contact should be handled as if capable of transmitting Tel: 1-888-362-2447 (1-888-DNA-CHIP) infection and disposed of with proper precautions in accordance Fax: 1-408-731-5441 with federal, state, and local regulations. This includes adherence to the OSHA Bloodborne Pathogens Standard (29 CFR 1910.1030) for Affymetrix UK Ltd blood-derived and other samples governed by this act. Never pipet by Voyager, Mercury Park, mouth. Avoid specimen contact with skin and mucous membranes. Wycombe Lane, Wooburn Green, 4. CAUTION: Exercise standard precautions when obtaining, handling, and High Wycombe HP10 0HH disposing of potentially carcinogenic reagents. United Kingdom 5. Exercise care to avoid cross-contamination of samples during all steps of this E-mail: [email protected] procedure, as this may lead to erroneous results. UK and Others Tel: +44 (0) 1628 552550 6. Use powder-free gloves whenever possible to minimize introduction of pow- France Tel: 0800919505 der particles into sample or probe array cartridges. Germany Tel: 01803001334 Fax: +44 (0) 1628 552585

Affymetrix Japan, K. K. STORAGE, HANDLING, AND STABILITY Mita NN Bldg, 16 Floor The GeneChip probe array consists of a square glass substrate mounted in a 4-1-23 Shiba, Minato-ku plastic cartridge (Figure 1). The glass contains an array of oligonucleotides that, Tokyo 108-0014, Japan when mounted, is on the inner glass surface. A chamber in the plastic housing E-mail: [email protected] directly under the glass acts as a reservoir where hybridization and washing Tel: +81-(0)3-5730-8200 occur. Fax: +81-(0)3-5730-8201 Although the inner glass surface of the probe array is protected, any con- Please visit our web site for international distributor contact information tamination or scratches on the outer surface of the glass can compromise the www.affymetrix.com accuracy of the scan. Avoid touching the surface of the glass with your ﬁ ngers. Skin oils and other substances, such as lotions or ink, can ﬂ uoresce. If the surface of the glass is noticeably dirty, it can be carefully cleaned with a non-abrasive TRADEMARKS laboratory tissue. Affymetrix®, ®, GeneChip®, HuSNP®, GenFlex®, Flying Objective™, CustomExpress®, CustomSeq®, NetAffx™, ‘The Way Ahead™’, ‘Tools to Take You As Far As Your Vision®’, ‘Powered by Affymetrix™’, and ‘GeneChip-compatible™’ are trademarks of Affymetrix, Inc.

LIMITED LICENSE Subject to the Affymetrix terms and conditions that govern your use of Affyme- trix products, Affymetrix grants you a non-exclusive, non-transferable, non- sublicensable license to use this Affymetrix product only in accordance with the manual and written instructions provided by Affymetrix. You understand and agree that except as expressly set forth in the Affymetrix terms and conditions, Figure 1. GeneChip® Probe Array that no right or license to any patent or other intellectual property owned or The GeneChip® probe arrays should be stored at 2° to 8°C. Refer to the licensable by Affymetrix is conveyed or implied by this Affymetrix product. expiration date on the package label. Do not use probe arrays or reagents after In particular, no right or license is conveyed or implied to use this Affymetrix the expiration date. product in combination with a product not provided, licensed or speciﬁ cally recommended by Affymetrix for such use.

PATENTS Products may be covered by one or more of the following patents and/or sold under license from Oxford Gene Technology: U.S. Patent Numbers 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.

GeneChip® Arabidopsis TTilingiling 11.0R.0R ArArrayray For Research Use Only 702235 RRev.ev. 1 Not for use in diagnostic procedures 004/064/06