Poster: Genomic & proteomic resources

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

Presenter:	Coughlan, Sean , sean_coughlan@agilent.com
Authors	Coughlan, Sean  (A)   Chang, Dustin  (A)   Meyers, Blake  (B) (B)  Agrawal, Vikas  (B) (B)
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. 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 bp in length, and can uniquely identify >85% of all genes in Arabidopsis. To date, eleven Arabidopsis thaliana MPSS libraries are available for analysis at the following URL (http://www.dbi.udel.edu/mpss). The in silico transcriptional data obtained from these libraries (callus, inflorescence, shoot, root, silique etc) has been compared to global gene expression data obtained by hybridization of cRNA derived from the same RNA populations. The DNA microarrays used were the Agilent Arabidopsis 3.0 microarray (44k format); this array contains 60-mers synthesized in situ array based on the 29,993 annotations in the TAIR ATH1 annotation (version 5.0). Another 11,000 features were included in the array which include both unannotated 10,000 transcripts identified by whole genome tiling arrays and by MPSS data, and about 1000 mi RNAs. We examined the detection limits of the Agilent microarray and detection system to measure changes in relative abundance of low (single) copy transcripts, by reference to the Arabidopsis MPSS database; the MPSS data identifies the specific genes from which the signatures are derived, and a quantitative abundance level in parts per million (PPM). We present our preliminary results from this comparison