ARS | Publication request: Description and analysis of the Bovine Gene Atlas - An extensive compendium of bovine transcript profiles

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: October 3, 2007
Publication Date: January 2, 2008
Citation: Harhay, G.P., Keele, J.W., Smith, T.P., Alexander, L.J., Matukumalli, L.K., Schroeder, S.G., Liu, G., Van Tassell, C.P., Sonstegard, T.S. 2008. Description and analysis of the Bovine Gene Atlas - An extensive compendium of bovine transcript profiles (abstract). Plant and Animal Genome XVI Conference. Poster No. P516.

Technical Abstract: The Bovine Gene Atlas (BGA) is a compendium of over 7.2 million unique 20-base transcript tags profiled from 81 tissues acquired from the cow “L1 Dominette 01449” (L1D), her male fetus, her 255-day-old heifer calf, and her father. The BGA tags were generated on a next-generation massively parallel sequencing platform. L1D’s genome (current build: 3.1) was sequenced at the Baylor College of Medicine and Genome Canada sequenced ESTs and full-length transcripts from her tissues. The 50% inbred Hereford cow and her first-degree relatives were chosen as a source of tissues to minimize sequence differences between tags and genomic or expressed sequence and increase the probability of unequivocally mapping tags to build 3.1. The BGA is comprised of cardiovascular, digestive, endocrine, lymphatic, muscular, nervous, reproductive, and urinary tissues sampled from animals in the fetal, juvenile, and adult stages of development. This report describes a computational pipeline and tools to map the BGA tags to build 3.1, view the tags positioned on the 3.1 build using GBrowse, and a new database schema for positional and functional queries. Consistency of the BGA tags with current gene models, apparent tissue-specific alternative splicing variability, and other observations will be presented.