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United States Department of Agriculture

Agricultural Research Service

Title: Characterization of Sequence Data from a Normalized Bovine Mammary Gland Cdna Library

Authors
item Van Tassell, Curtis
item Sonstegard, Tad
item Capuco, Anthony
item Ashwell, Melissa
item Wells, Kevin

Submitted to: Beltsville Agricultural Research Center Symposium
Publication Type: Abstract Only
Publication Acceptance Date: September 5, 2000
Publication Date: September 10, 2000
Citation: Van Tassell, C.P., Sonstegard, T.S., Capuco, A.V., Ashwell, M.S., Wells, K.D. 2000. Characterization of sequence data from a normalized bovine mammary gland cdna library [abstract]. Beltsville Symposium XXIV - Healthy Animals 2000. p. 19.

Technical Abstract: Characterization of mammary-specific gene expression will aid discovery of biological factors that influence production and udder health in dairy animals. Expressed sequence tags (EST) are a critical component of this investigation, serving as a resource for gene discovery, mapping, and expression profiling. To generate 10,000 unique bovine mammary EST, a normalized cDNA library was constructed that represented gene expression from 8 different stages of mammary growth, development, and health. Equal amounts of mRNA isolated from udder biopsies at each stage were combined used to synthesize cDNA. To facilitate high-throughput sequencing 55,296 clones were picked and arrayed into 384-well plates. To date, a total of 21,594 clones have been single-pass sequenced. Of those, 14,122 sequences were submitted to GenBank, 7,466 rejected for insufficient high quality sequence length, and 6 rejected due to low complexity sequence. Basic local lalignment search tool (BLAST) analysis of the sequencing data from the first 12,129 EST was performed. BLAST analysis was performed on sequences within the library to assess diversity within the library. BLAST analysis against the GenBank nr and dbEST was used to evaluate the redundancy of the library compared to publicly available sequences. Sixty one percent of the sequences were considered unique within the library (match score < 200). Of the uniquely identified EST, 41% had no similarity to bovine GenBank sequence, and 4% had no known identity to any GenBank sequence. For the EST with similarity to published bovine EST (55%), greater than 85% of these were redundant with EST generated from one of the four bovine cDNA libraries at ARS-USDA-MARC. The EST sequence data indicate this library is an important source of unique mammary gland EST.

Last Modified: 4/19/2014