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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC AND BIOLOGICAL DETERMINANTS OF RESPIRATORY DISEASE SUSCEPTIBILITY Title: A Digital Gene Expression-Based Bovine Gene Atlas Evaluating 92 Adult, Juvenile and Fetal Cattle Tissues

Authors
item Harhay, Gregory
item Alexander, Leeson
item Smith, Timothy
item Matukumalli, Lakshmi -
item Schroeder, Steven
item Sonstegard, Tad

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: January 20, 2010
Publication Date: February 24, 2010
Citation: Harhay, G.P., Alexander, L.J., Smith, T.P.L., Matukumalli, L.K., Schroeder, S.G., Sonstegard, T.S. 2010. A Digital Gene Expression-Based Bovine Gene Atlas Evaluating 92 Adult, Juvenile and Fetal Cattle Tissues [abstract]. In: Proceedings of the Advances in Genome Biology & Technology Conference, February 24-27, 2010, Marco Island, Florida. p. 67.

Technical Abstract: A comprehensive transcriptome survey, or “Gene Atlas,” provides information essential for a complete understanding of the genomic biology of an organism. Using a digital gene expression approach, we developed a Gene Atlas of RNA abundance in 92 adult, juvenile and fetal cattle tissues. The samples were collected primarily from the cow used to generate the genome sequence, her sire, male fetus and female calf, in order to reduce the impact of polymorphisms in tag sequences on genome sequence-dependent analysis. RNA abundance was determined by digestion of double-stranded cDNA with DpnII, followed by generation of adjacent 16-base “tags” for sequencing on the Illumina platform. One channel on the instrument was used for each tissue, generating 7.3 million unique tag sequences (300 million total tags). Abundance of each unique tag sequence was expressed as tags per million (tpm); only tag sequences of more than two tpm in a single tissue, or tags present at lower tpm but appearing in at least ten tissues, were further analyzed. Using this filter, a set of 227,481 distinct tag sequences were found that uniquely mapped to the genome (TUMG) that accounted for 63% of the total tag abundance. From the TUMG, 87,764 unique tag sequences could be unambiguously associated with 16,517 annotated protein-coding loci in the bovine draft genome that accounted for 45% of the total tag abundance. There were 5,429 annotated loci constitutively expressed (observed in all tissues) from a 45,178-tag subset of the TUMG that mapped within these loci. Similarly, there were 8,694 constitutively expressed unique tag sequences mapping within 4,610 distinct loci and 3,445 constitutively expressed unique tags mapping outside annotated gene boundaries that represent a resource for enhancing current gene models. The data can be examined in a genomic context at http://www.agbase.msstate.edu/bovineatlas

Last Modified: 7/31/2014
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