NDLI: AGRONOMICS1: A New Resource for Arabidopsis Transcriptome Profiling1 [W] [OA]

Content Provider	PubMed Central
Author	Hubert, Rehrauer Aquino, Catharine Wilhelm, Gruissem Henz, Stefan R. Hilson, Pierre Laubinger, Sascha Naira, Naouar Patrignani, Andrea Stephane, Rombauts Shu, Huan Peer, Yves Van De Vuylsteke, Marnik Weigel, Detlef Zeller, Georg Hennig, Lars
Copyright Year	2010
Abstract	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.
Related Links	http://dx.doi.org/10.1104/pp.109.150185
Ending Page	499
Page Count	13
Starting Page	487
File Format	PDF
ISSN	00320889
e-ISSN	15322548
Journal	Plant Physiology
Issue Number	2
Volume Number	152
Language	English
Publisher	American Society of Plant Biologists
Publisher Date	2010-02-01
Access Restriction	Open
Rights Holder	American Society of Plant Biologists
Subject Keyword	Plant Science Genetics Physiology Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Genetics Physiology Plant Science

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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AGRONOMICS1: A New Resource for Arabidopsis Transcriptome Profiling

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