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PRODUCT BULLETIN GeneAssist™ Pathway Atlas GeneAssist™ Pathway Atlas www.ambion.com/tools/geneassist • Learn how your protein is involved in different cellular pathways • Find the interrelationships between proteins in a pathway • Over 350 different pathways are currently available • Illustrations show molecular interactions and cellular compartments • View gene, disease, and product information by selecting proteins within the illustration • Quickly and easily find and order Silencer® siRNAs and the corresponding TaqMan® Gene Expression Assays The GeneAssist™ Pathway Atlas. From Products to Proteins Cell signaling, metabolic, and disease pathway maps are becoming increasingly intricate as more genes and proteins are mapped to cellular functions. As a result, there is a growing need to understand which pathways involve certain genes, as well as the interrelationships between the proteins within those pathways. The GeneAssist™ Pathway Atlas meets these demands by providing more than 350 interactive pathway maps along with detailed gene and protein information for each protein in the pathway. For easy product ordering, an interface is included which reports the recommended Silencer® siRNAs for gene silencing and the corresponding TaqMan® Gene Expression Assays. Search or Browse by Pathway Inside GeneAssist™ Pathway Atlas, you will find more than 350 easy-to-understand signal transduction, metabolic and disease state pathway maps. The pathways can be browsed alphabetically by name or searched using keywords or gene identifiers such as Entrez Gene ID, gene name, gene symbol, or NCBI transcript accession number (Figure 1). Once a pathway is selected, the results are presented in the Pathway Map illustration showing all proteins known in the pathway and their interactions in the appropriate cellular compartments (Figure 2). On this page, you will also find a link to an overview of the pathway with references (Figure 3, Pathway Overview Page). Detailed Gene and Protein Information From the Pathway Map, just click on any protein or protein complex to access the Protein and Gene Information page containing the corresponding protein and gene identifiers, Silencer®siRNAs, and TaqMan® Gene Expression Assays. The example in Figure 4 shows the detailed information for the Protein Family: HRas, KRas2, NRas, RRas, MRas, RRase2. At the top of the page is general information on the genes. Choosing “Gene ID” or one of the “Transcripts” listed takes you to the relevant NCBI information pages. As shown in Figure 5, the “Disease Information” link reveals details on the protein and its role in various disease processes along with the relevant references. Select Gene-specific Products On the right of the Protein and Gene Information page is the product ordering information for Silencer® siRNAs and TaqMan® Gene Expression Assays corresponding to the selected gene. To simplify the product selection process, three siRNAs and a single TaqMan Gene Expression Assay are recommended for each gene, and can be added to an online shopping basket directly from this page. Where available, validated siRNAs are listed with links to the validation data. These siRNAs have been empirically tested and proven to knock down expression of the target gene. In many cases, more than three siRNAs and a single TaqMan Gene Expression Assay are available for a given target. These products can be accessed by clicking on the “Show Additional siRNAs” or the “Show Additional Assays”, respectively. View siRNA Target and TaqMan Primer/Probe Binding Sites To view the siRNA target and/or TaqMan primer and probe binding sites along the gene transcript, select the “View Alignment Map” link. This brings up an interactive graphical representation of the gene of interest (Figure 6). The default option shows RefSeq transcripts; however, you can also view GenBank mRNAs, giving you the freedom to identify siRNAs and assays that target non-RefSeq transcripts. Figure 1. Search/browse by pathway, gene name, ID, symbol or NCBI transcript. Figure 2. Pathway Map Page. Figure 3. Pathway Overview Page. Figure 4. ProteinGene Information Page. Link to disease information page (yellow) Links to NCBI Entrez (orange) Order Online Products selected within the GeneAssist™ Pathway Atlas are simply added to an Applied Biosystems shopping basket. If you already have an existing Applied Biosystems basket in progress, you have the option to add those items to that basket (select “Append to Existing Basket”), or create a new basket. After you are finished selecting your siRNAs and TaqMan® Gene Expression Assays, you can continue shopping on the Applied Biosystems website for most Ambion and Applied Biosytems products, and then check out all your items together in a convenient, single transaction.* *Please note that the online ordering basket within GeneAssist™ is an Simplify Gene Silencing Experiments Silencer ® Pre-designed siRNAs • Ready to use siRNAs for human, mouse, and rat genes • Searchable database makes it simple to find siRNAs to your genes of interest • Efficient gene knockdown guaranteed Find Silencer Pre-designed siRNAs and corresponding TaqMan® Gene Expression Assays on the web at www.ambion.com/info/siRNA. Applied Biosystems basket, and not an Ambion basket. Items ordered on the Ambion website outside of the GeneAssist™ tool go through a separate checkout process and cannot be combined with a new or existing Applied Biosystems basket. Verify Gene Silencing Figure 5. Disease Information Page. TaqMan® Gene Expression Assays • Gene-specific TaqMan® probe and primer sets for quantitative gene expression studies in human, mouse, rat, Rhesus, C. elegans, Drosophila, and Arabidopsis • Convenient single tube format and 20X formulation • Universal thermal cycling conditions Find TaqMan Gene Expression Assays and corresponding Silencer siRNAs for your genes of interest at www.allgenes.com. Figure 6. Alignment Map Box . For research use only. Not for use in diagnostic procedures. Ambion siRNA products are manufactured under license from the Massachusetts Institute of Technology to U.S. Patent Nos. 7,056,704 and 7,078,196 and pending counterparts, and is provided for research or educational purposes only. ORDERING INFORMATION Description Quantity Silencer ® Pre-designed siRNA, standard purity 20 nmol AM16704 Silencer ® Pre-designed siRNA, standard purity 5 nmol AM16708 Silencer Pre-designed siRNA, standard purity (when 3 or more are purchased to the same target) 5 nmol AM16708A Silencer ® Pre-designed siRNA, HPLC purified 40 nmol AM16804 Silencer ® Validated siRNA, standard purity 5 nmol AM51331 Silencer Validated siRNA, standard purity 20 nmol AM51333 TaqMan ® Gene Expression Assays (Inventoried) 250 x 20 µL rxns ® ® Part Number 4331182 Silencer® siRNAs and TaqMan® Assays - Proven Performance. Proven Together. With RNA interference, you can elucidate gene function in a matter of days using the most complete suite of premium quality reagents available for RNA experiments from Applied Biosystems and Ambion, an Applied Biosystems Business. Our potent, pre-designed siRNAs, optimized qRT-PCR gene expression assays and reagents and the protocols provided with them, streamline each step of an RNAi experiment. The result? Reduced technical variability in your experiments, full technical support across you RNAi application, and freedom to focus on making critical biological discoveries! For more information, order “Using siRNAs to Delineate Gene Function: A Step-by-Step Guide” on-line at www.ambion.com/litreq or contact your local sales representative. Ask for 137AP01-01. For Research Use Only. Not for use in diagnostic procedures. © Copyright 2007, Applied Biosystems. All rights reserved. Applied Biosystems and AB (Design) are registered trademarks and GeneAssist is a trademark of Applera Corporation or its subsidiaries in the U.S. and/or certain other countries. Ambion and Silencer are registered trademarks of Ambion, Inc., an Applied Biosystems Business in the U.S. and/or certain other countries. TaqMan is a registered trademark of Roche Molecular Systems. Printed in the USA, 01/2007 Publication 137PB22-01 Headquarters 850 Lincoln Centre Drive | Foster City, CA 94404 USA Phone 650.638.5800 | Toll Free 800.345.5224 www.appliedbiosystems.com International Sales For our office locations please call the division headquarters or refer to our Web site at www.appliedbiosystems.com/about/offices.cfm