High-throughput gene discovery in the rat

Todd E Scheetz, Jennifer J Laffin, Brian Berger, Sara Holte, Susan A Baumes, Robert Brown, Shereen Chang, Justin Coco, Jim Conklin, Keith Crouch, Micca Donohue, Greg Doonan, Chris Estes, Mari Eyestone, Katrina Fishler, Jack Gardiner, Lankai Guo, Brad Johnson, Catherine Keppel, Rikki KregerMark Lebeck, Rudy Marcelino, Vladan Miljkovich, Mindee Perdue, Ling Qui, Joshua Rehmann, Rebecca S Reiter, Bridgette Rhoads, Kelly Schaefer, Christina Smith, Ivana Sunjevaric, Kurtis Trout, Ning Wu, Clayton L Birkett, Jared Bischof, Barry Gackle, Allen Gavin, A Jason Grundstad, Brian Mokrzycki, Chris Moressi, Brian O'Leary, Kevin Pedretti, Chad Roberts, Natalie L Robinson, Michael Smith, Dylan Tack, Nishank Trivedi, Tamara Kucaba, Tom Freeman, Jim J-C Lin, Maria F Bonaldo, Thomas L Casavant, Val C Sheffield, M Bento Soares

Research output: Contribution to journalArticlepeer-review

Abstract

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.
Original languageEnglish
Pages (from-to)733-41
Number of pages9
JournalGenome Research
Volume14
Issue number4
DOIs
Publication statusPublished - Apr 2004

Keywords

  • Animals
  • DNA, Complementary
  • Expressed Sequence Tags
  • Female
  • Gene Library
  • Genes
  • Humans
  • Male
  • Mice
  • Polyadenylation
  • RNA Processing, Post-Transcriptional
  • Rats
  • Rats, Sprague-Dawley
  • Sequence Analysis, DNA
  • Software

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