2007 Annual Report 1a.Objectives (from AD-416) Build a bovine gene atlas using gene expression analysis data derived from 100 tissues of the genome cow and her relatives. 1b.Approach (from AD-416) Combined gene expression analysis using data from 16 MPSS libraries and 100 oligo based microarrays. 3.Progress Report This report documents research conducted under a Reimbursable Agreement between ARS and NRI. The funding proposal number is 2005-05011 from the USDA NRI-CGP 43.1 Animal Genome Reagent and Tool Development. Award money was disbursed in February 2006 to the Beltsville Area. USDA, ARS, USMARC and LARRL research centers are also participating in this project. Additional details of the research can be found in the report for the parent project 1265-31000-081-00D, “Identification, validation and fine-mapping of quantitative trait loci in dairy cattle.” Total RNA from 100 tissues derived from the genome sequence cow (Line 1 Hereford) and her offspring were checked for integrity and quality. These samples were then shipped to Illumina (Hayward, CA) and cDNA libraries were made from each tissue for populating the flow cells of the next generation sequencing platform. These flow cells will be used to generate the sequence tags (20 bp) from each tissue to characterize levels of gene expression. In collaboration with USMARC, a database and user friendly front end to the database were developed and tested using a preliminary set of test tag data generated from six of the RNA samples. Illumina took steps to improve the cDNA library preparation to remove unwanted adaptor sequences, thus increasing the depth of sequencing from each tissue. To date, sequence tag data from approximately 40 libraries now resides in redundant databases at USMARC and BFGL. This project will be completed in Dec., 2007. Monitoring activities associated with this project included annual updates presented to CSREES-NRI NPS in conjunction with Plant and Animal Genome Conferences and submission to CSREES-NRI of an annual progress report. This research continues to support two objectives of its related in-house project to develop biological resources and computational tools to enhance characterization of the bovine genome sequence (objective #1) and to characterize conserved genome elements and identify functional genetic variation (objective #3).