High-throughput gene discovery in the rat.
The rat is an important animal model for human diseases and is widely used in physiology. In this article we present a new strategy for gene discovery based on the production of ESTs from serially subtracted and normalized cDNA libraries, and we describe its application for the development of a comprehensive nonredundant collection of rat ESTs. Our new strategy appears to yield substantially more EST clusters per ESTs sequenced than do previous approaches that did not use serial subtraction. However, multiple rounds of library subtraction resulted in high frequencies of otherwise rare internally primed cDNAs, defining the limits of this powerful approach. To date, we have generated >200,000 3' ESTs from >100 cDNA libraries representing a wide range of tissues and developmental stages of the laboratory rat. Most importantly, we have contributed to approximately 50,000 rat UniGene clusters. We have identified, arrayed, and derived 5' ESTs from >30,000 unique rat cDNA clones. Complete information, including radiation hybrid mapping data, is also maintained locally at http://genome.uiowa.edu/clcg.html. All of the sequences described in this article have been submitted to the dbEST division of the NCBI.
Scheetz
Todd E
TE
Center for Bioinformatics and Computational Biology, The University of Iowa, Iowa City, Iowa 52242, USA. tscheetz@eng.uiowa.edu
Laffin
Jennifer J
JJ
Berger
Brian
B
Holte
Sara
S
Baumes
Susan A
SA
Brown
Robert
R
Chang
Shereen
S
Coco
Justin
J
Conklin
Jim
J
Crouch
Keith
K
Donohue
Micca
M
Doonan
Greg
G
Estes
Chris
C
Eyestone
Mari
M
Fishler
Katrina
K
Gardiner
Jack
J
Guo
Lankai
L
Johnson
Brad
B
Keppel
Catherine
C
Kreger
Rikki
R
Lebeck
Mark
M
Marcelino
Rudy
R
Miljkovich
Vladan
V
Perdue
Mindee
M
Qui
Ling
L
Rehmann
Joshua
J
Reiter
Rebecca S
RS
Rhoads
Bridgette
B
Schaefer
Kelly
K
Smith
Christina
C
Sunjevaric
Ivana
I
Trout
Kurtis
K
Wu
Ning
N
Birkett
Clayton L
CL
Bischof
Jared
J
Gackle
Barry
B
Gavin
Allen
A
Grundstad
A Jason
AJ
Mokrzycki
Brian
B
Moressi
Chris
C
O'Leary
Brian
B
Pedretti
Kevin
K
Roberts
Chad
C
Robinson
Natalie L
NL
Smith
Michael
M
Tack
Dylan
D
Trivedi
Nishank
N
Kucaba
Tamara
T
Freeman
Tom
T
Lin
Jim J-C
JJ
Bonaldo
Maria F
MF
Casavant
Thomas L
TL
Sheffield
Val C
VC
Soares
M Bento
MB
D000818:Animals; D018076:DNA, Complementary / Q000235:genetics; D020224:Expressed Sequence Tags; D005260:Female; D015723:Gene Library; D005796:Genes / Q000235:genetics*; D006801:Humans; D008297:Male; D051379:Mice; D026723:Polyadenylation / Q000235:genetics; D012323:RNA Processing, Post-Transcriptional / Q000235:genetics; D051381:Rats; D017207:Rats, Sprague-Dawley; D017422:Sequence Analysis, DNA / Q000379:methods / Q000706:statistics & numerical data; D012984:Software
D018076:DNA, Complementary