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          Institute: MPI für Entwicklungsbiologie     Collection: Abteilung 6 - Molecular Biology (D. Weigel)     Display Documents



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ID: 561631.0, MPI für Entwicklungsbiologie / Abteilung 6 - Molecular Biology (D. Weigel)
AGRONOMICS1: A New Resource for Arabidopsis Transcriptome Profiling
Authors:Rehrauer, H.; Aquino, C.; Gruissem, W.; Henz, S. R.; Hilson, P.; Laubinger, S.; Naouar, N.; Patrignani, A.; Rombauts, S.; Shu, H.; Van de Peer, Y.; Vuylsteke, M.; Weigel, D.; Zeller, G.; Hennig, L.
Date of Publication (YYYY-MM-DD):2010-02
Title of Journal:Plant Physiology
Volume:152
Issue / Number:2
Start Page:487
End Page:499
Review Status:not specified
Audience:Not Specified
Abstract / Description: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.
Free Keywords:brassica self-incompatibility; DNA methylation; expression analysis; gene-expression; histone methylation; tiling-arrays; rice genome; chip-chip; rna-seq; thaliana
External Publication Status:published
Document Type:Article
Affiliations:MPI für Entwicklungsbiologie/Abteilung 6 - Molekulare Biologie (Detlef Weigel)
External Affiliations:ETH, Dept Biol, CH-8092 Zurich, Switzerland ETH, Dept Biol, CH-8092 Zurich, Switzerland ETH, Dept Biol, CH-8092 Zurich, Switzerland ETH, Zurich Basel Plant Sci Ctr, CH-8092 Zurich, Switzerland Univ Zurich, CH-8057 Zurich, Switzerland ETH, Funct Genom Ctr Zurich, CH-8057 Zurich, Switzerland Max Planck Inst Dev Biol, Dept Mol Biol, D-72076 Tubingen, Germany Univ Ghent VIB, Dept Plant Syst Biol, B-9052 Ghent, Belgium Univ Ghent, Dept Plant Biotechnol & Genet, B-9052 Ghent, Belgium %G English
Identifiers:ISSN:0032-0889 %R DOI 10.1104/pp.109.150185 [ID No:1]
ISI:000274246600011 [ID No:2]
ISI:000274246600011 [ID No:3]
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