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Abstract Detail


Large Scale Technologies and Resources

Underwood, Beverly [1], Xiao, Yongli [2], Redman, Julia [2], Wu, Hank [2], Wang, Wei [2], Moskal, William [2], Monaghan, Erin [2], Town, Christopher [2].

Completing the Expression Catalog of the Arabidopsis Transcriptome by Quantitative Real Time PCR.

Five sequential rounds of whole genome annotation at TIGR and one at TAIR have produced a dataset that contains structural and functional annotation for 26,751 protein coding genes of which over 8,000 have both molecular function and biological process annotated as unknown. Although the method has not yet been applied to large-scale annotation in Arabidopsis, it is possible to infer potential functions for many of these genes by correlation of their expression patterns with known genes and pathways.  Publicly available datasets from Affymetrix ATH1 expression array combined with massively parallel signature sequencing have provided statistically significant expression values over diverse tissues for just over 22,000 distinct protein-coding genes. Because many of the genes of unknown function are expressed at levels that are too low to be effectively profiled by hybridization-based methods, our current NSF 2010 project is to generate expression profiles by quantitative real time PCR for 4,000+ Arabidopsis genes for which expression data are unavailable. To date, we have performed quantitative real time PCR on over 1,000 genes that either lack reliable expression data from or are not represented on the ATH1 array using cDNAs from leaf, root and T87 cell culture and seedlings treated with IAA, SA and salt. Over 90% of the genes were expressed in at least one of our current cDNA populations and ~ 40% of them showed differential expression in at least 2 out of 6 conditions. In addition, we have developed a high throughput pipeline to generate promoter-reporter constructs and transgenic Arabidopsis plants for 1,000 genes of unknown function. So far, all the detected GFP expression patterns in these transgenic plants are localized to small regions of tissues and cell types. Both the qPCR and reporter construct data can be found at www.tigr.org/tdb/e2k1/ath1/qpcr/index.shtml. Research supported by the NSF 2010 Project


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Related Links:
Expression Profiling Project Website


1 - The Institute for Genomic Research, A Division of the J Craig Venter I, Plant Genomics, 9712 Medical Center Drive, Rockville, MD, 20850, USA
2 - The Institute for Genomic Research, A Division of the J Craig Venter I, Plant Genomics

Keywords:
transcriptome
promoter
expression
reporter
unknown.

Presentation Type: Plant Biology Abstract
Session: P
Location: Exhibit Hall (Northeast, Southwest & Southeast)/Hilton
Date: Sunday, July 8th, 2007
Time: 8:00 AM
Number: P42010
Abstract ID:1622


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