| AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling. | |
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MedLine Citation:
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PMID: 20032078 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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Transcriptome profiling has become a routine tool in biology. For Arabidopsis (Arabidopsis thaliana), the Affymetrix ATH1 expression array is most commonly used, but it lacks about one-third of all annotated genes present in the reference strain. An alternative are tiling arrays, but previous designs have not allowed the simultaneous analysis of both strands on a single array. We introduce AGRONOMICS1, a new Affymetrix Arabidopsis microarray that contains the complete paths of both genome strands, with on average one 25mer probe per 35-bp genome sequence window. In addition, the new AGRONOMICS1 array contains all perfect match probes from the original ATH1 array, allowing for seamless integration of the very large existing ATH1 knowledge base. The AGRONOMICS1 array can be used for diverse functional genomics applications such as reliable expression profiling of more than 30,000 genes, detection of alternative splicing, and chromatin immunoprecipitation coupled to microarrays (ChIP-chip). Here, we describe the design of the array and compare its performance with that of the ATH1 array. We find results from both microarrays to be of similar quality, but AGRONOMICS1 arrays yield robust expression information for many more genes, as expected. Analysis of the ATH1 probes on AGRONOMICS1 arrays produces results that closely mirror those of ATH1 arrays. Finally, the AGRONOMICS1 array is shown to be useful for ChIP-chip experiments. We show that heterochromatic H3K9me2 is strongly confined to the gene body of target genes in euchromatic chromosome regions, suggesting that spreading of heterochromatin is limited outside of pericentromeric regions. |
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Authors:
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Hubert Rehrauer; Catharine Aquino; Wilhelm Gruissem; Stefan R Henz; Pierre Hilson; Sascha Laubinger; Naira Naouar; Andrea Patrignani; Stephane Rombauts; Huan Shu; Yves Van de Peer; Marnik Vuylsteke; Detlef Weigel; Georg Zeller; Lars Hennig |
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Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't Date: 2009-12-23 |
Journal Detail:
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Title: Plant physiology Volume: 152 ISSN: 1532-2548 ISO Abbreviation: Plant Physiol. Publication Date: 2010 Feb |
Date Detail:
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Created Date: 2010-02-04 Completed Date: 2010-03-22 Revised Date: 2010-09-28 |
Medline Journal Info:
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Nlm Unique ID: 0401224 Medline TA: Plant Physiol Country: United States |
Other Details:
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Languages: eng Pagination: 487-99 Citation Subset: IM |
Affiliation:
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Functional Genomics Center Zurich, ETH and University of Zurich, CH-8057 Zurich, Switzerland. |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Arabidopsis
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genetics* Chromatin Immunoprecipitation Computational Biology DNA Probes Gene Expression Profiling / methods* Genes, Plant Genomics Oligonucleotide Array Sequence Analysis / methods* RNA, Plant / genetics Sequence Analysis, DNA |
| Chemical | |
Reg. No./Substance:
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0/DNA Probes; 0/RNA, Plant |
| Comments/Corrections | |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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