Journal article
High-throughput gene discovery in the rat
Genome research, Vol.14(4), pp.733-741
04/2004
DOI: 10.1101/gr.1414204
PMCID: PMC383320
PMID: 15060017
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.
Details
- Title: Subtitle
- High-throughput gene discovery in the rat
- Creators
- Katrina FishlerJack GardinerLankai GuoBrad JohnsonCatherine KeppelRikki KregerMark LebeckRudy MarcelinoVladan MiljkovichMindee PerdueLing QuiJoshua RehmannRebecca S ReiterBridgette RhoadsKelly SchaeferChristina SmithIvana SunjevaricKurtis TroutNing WuClayton L BirkettJared BischofBarry GackleAllen GavinA Jason GrundstadBrian MokrzyckiChris MoressiBrian O'LearyTodd E Scheetz - Center for Bioinformatics and Computational Biology, The University of Iowa, Iowa City, Iowa 52242, USA. tscheetz@eng.uiowa.eduKevin PedrettiJennifer J LaffinBrian BergerChad RobertsSara HolteNatalie L RobinsonSusan A BaumesMichael SmithRobert Brown II - University of IowaDylan TackNishank TrivediShereen ChangJustin CocoTamara KucabaJim ConklinTom FreemanJim J-C Lin - University of Iowa, BiologyKeith CrouchMicca DonohueMaria F BonaldoGreg DoonanThomas L Casavant - University of Iowa, Center for Bioinformatics and Computational BiologyVal C Sheffield - University of Iowa, Stead Family Department of PediatricsChris EstesM Bento SoaresMari Eyestone
- Resource Type
- Journal article
- Publication Details
- Genome research, Vol.14(4), pp.733-741
- DOI
- 10.1101/gr.1414204
- PMID
- 15060017
- PMCID
- PMC383320
- NLM abbreviation
- Genome Res
- ISSN
- 1088-9051
- eISSN
- 1549-5469
- Publisher
- United States
- Grant note
- 2R01-HL597898 / NHLBI NIH HHS
- Language
- English
- Date published
- 04/2004
- Academic Unit
- Roy J. Carver Department of Biomedical Engineering; Electrical and Computer Engineering; Stead Family Department of Pediatrics; Pathology; Iowa Neuroscience Institute; Medical Genetics and Genomics; Biology; Family and Community Medicine; Ophthalmology and Visual Sciences
- Record Identifier
- 9983979966402771
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