{[ promptMessage ]}

Bookmark it

{[ promptMessage ]}

Gene Expression Analyses of Arabidopsis Chromosome 2 Using a Genomic DNA Amplicon Microarray

Gene Expression Analyses of Arabidopsis Chromosome 2 Using a Genomic DNA Amplicon Microarray

Info icon This preview shows pages 1–3. Sign up to view the full content.

View Full Document Right Arrow Icon
10.1101/gr.552003 Access the most recent version at doi: 2003 13: 327-340 Genome Res. Heenam Kim, Erik C. Snesrud, Brian Haas, Foo Cheung, Christopher D. Town and John Quackenbush Genomic DNA Amplicon Microarray Chromosome 2 Using a Arabidopsis Gene Expression Analyses of References http://www.genome.org/cgi/content/full/13/3/327#otherarticles Article cited in: http://www.genome.org/cgi/content/full/13/3/327#References This article cites 46 articles, 18 of which can be accessed free at: service Email alerting click here top right corner of the article or Receive free email alerts when new articles cite this article - sign up in the box at the Notes http://www.genome.org/subscriptions/ go to: Genome Research To subscribe to © 2003 Cold Spring Harbor Laboratory Press on November 28, 2006 www.genome.org Downloaded from
Image of page 1

Info icon This preview has intentionally blurred sections. Sign up to view the full version.

View Full Document Right Arrow Icon
Gene Expression Analyses of Arabidopsis Chromosome 2 Using a Genomic DNA Amplicon Microarray Heenam Kim, 1 Erik C. Snesrud, 1 Brian Haas, Foo Cheung, Christopher D. Town, and John Quackenbush 2 The Institute for Genomic Research, Rockville, MD 20850, USA. The gene predictions and accompanying functional assignments resulting from the sequencing and annotation of a genome represent hypotheses that can be tested and used to develop a more complete understanding of the organism and its biology. In the model plant Arabidopsis thaliana , we developed a novel approach to constructing whole-genome microarrays based on PCR amplification of the 3 ends of each predicted gene from genomic DNA, and constructed an array representing more than 94% of the predicted genes and pseudogenes on chromosome 2. With this array, we examined various tissues and physiological conditions, providing expression-based validation for 84% of the gene predictions and providing clues as to the functions of many predicted genes. Further, by examining the distribution of expression along the physical chromosome, we were able to identify a region of repressed transcription that may represent a previously undescribed heterochromatic region. [The sequence data from this study have been submitted to ArrayExpress under accession nos.: For the Array Design, A-TIGR-2. For the three subgroups of experiments: AbioticStress, E-TIGR-2; BioticStress, E-TIGR-3; Tissues, E-TIGR-4.] The sequencing of the whole Arabidopsis genome by an inter- national consortium, Arabidopsis Genome Initiative (AGI), be- gan in 1996. Chromosomes 2 and 4 were published in De- cember 1999 (Lin et al. 1999; Mayer et al. 1999), and the remainder of the genome, chromosomes 1, 3, and 5, was com- pleted and published in the winter of 2000 ( Arabidopsis Ge- nome Initiative 2000; European Union Chromosome 3 Ara- bidopsis Sequencing Consortium 2000; Kazusa DNA Research Institute et al. 2000; Theologis et al. 2000). The goal of a genome project is not the collection of the organism’s DNA sequence, but rather the identification of the genes encoded within. Consequently, as the Arabidopsis sequence became available, significant effort was devoted to gene prediction and sequence annotation. Gene identification in eukaryotes
Image of page 2
Image of page 3
This is the end of the preview. Sign up to access the rest of the document.

{[ snackBarMessage ]}

What students are saying

  • Left Quote Icon

    As a current student on this bumpy collegiate pathway, I stumbled upon Course Hero, where I can find study resources for nearly all my courses, get online help from tutors 24/7, and even share my old projects, papers, and lecture notes with other students.

    Student Picture

    Kiran Temple University Fox School of Business ‘17, Course Hero Intern

  • Left Quote Icon

    I cannot even describe how much Course Hero helped me this summer. It’s truly become something I can always rely on and help me. In the end, I was not only able to survive summer classes, but I was able to thrive thanks to Course Hero.

    Student Picture

    Dana University of Pennsylvania ‘17, Course Hero Intern

  • Left Quote Icon

    The ability to access any university’s resources through Course Hero proved invaluable in my case. I was behind on Tulane coursework and actually used UCLA’s materials to help me move forward and get everything together on time.

    Student Picture

    Jill Tulane University ‘16, Course Hero Intern