Poster: Emerging Technologies

Abs # 884: A Comparison of Global gene Expression and MPSS profiling in Arabidopsis thaliana.

Presenter:	Coughlan, Sean J, sean.j.coughlan@agilent.com
Authors	Coughlan, Sean J (A)   Myers, Blake  (B)   Cifuentes, Francisco  (A)
Affiliations:	(A): agilent technologies Inc (B): University of Delaware

MPSS stands for Massively Parallel Signature Sequencing, a technique invented and commercialized by Lynx Therapeutics, Inc. of Hayward, California. Brenner et al. (Nature Biotechnol have described MPSS and related technologies in publications. [2000] 18:630-634, and PNAS [2000] 97:1665-1670). Like SAGE (Serial Analysis of Gene Expression), MPSS produces short sequence tags produced from a defined position within an mRNA, and the relative abundance of these tags in a given library represents a quantitative estimate of expression of that gene. The MPSS tags are 17-23bp in length, and can uniquely identify >95% of all genes in Arabidopsis. To date five Arabidopsis thaliana MPSS libraries are available for analysis at the following URL (http://mpss.ucdavis.edu/nonjava.html). The in silico transcriptome data obtained from these (callus, inflorescence, shoot, root, silique) has been compared to global gene expression data obtained by hybridization of cRNA derived from the same RNA populations used to construct the MPSS libraries. The DNA micro arrays used were both the Agilent Arabidopsis I oligo deposition micro array and the new genome wide Arabidopsis thaliana 60mer in situ array based on the 29,252 annotations in the TAIR AT-transcript database. In particular we examined the detection limits of the Agilent micro array and detection system to measure changes in relative abundance of low (single) copy transcripts, by reference to the Arabidopsis MPSS database