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Title: A drosophila full-length cDNA resource

Abstract

Background: A collection of sequenced full-length cDNAs is an important resource both for functional genomics studies and for the determination of the intron-exon structure of genes. Providing this resource to the Drosophila melanogaster research community has been a long-term goal of the Berkeley Drosophila Genome Project. We have previously described the Drosophila Gene Collection (DGC), a set of putative full-length cDNAs that was produced by generating and analyzing over 250,000 expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages. Results: We have generated high-quality full-insert sequence for 8,921 clones in the DGC. We compared the sequence of these clones to the annotated Release 3 genomic sequence, and identified more than 5,300 cDNAs that contain a complete and accurate protein-coding sequence. This corresponds to at least one splice form for 40 percent of the predicted D. melanogaster genes. We also identified potential new cases of RNA editing. Conclusions: We show that comparison of cDNA sequences to a high-quality annotated genomic sequence is an effective approach to identifying and eliminating defective clones from a cDNA collection and ensure its utility for experimentation. Clones were eliminated either because they carry single nucleotide discrepancies, which most probably result from reversemore » transcriptase errors, or because they are truncated and contain only part of the protein-coding sequence.« less

Authors:
; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Laboratory Directed Research and Development; National Institutes of Health (US)
OSTI Identifier:
813593
Report Number(s):
LBNL-52636
R&D Project: 80ADLE; TRN: US200316%%279
DOE Contract Number:  
AC03-76SF00098
Resource Type:
Journal Article
Journal Name:
Genome Biology
Additional Journal Information:
Journal Volume: 3; Journal Issue: 12; Other Information: Journal Publication Date: December 2002; PBD: 9 May 2003
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; DROSOPHILA; FUNCTIONALS; GENES; NUCLEOTIDES; RNA

Citation Formats

Stapleton, Mark, Carlson, Joseph, Brokstein, Peter, Yu, Charles, Champe, Mark, George, Reed, Guarin, Hannibal, Kronmiller, Brent, Pacleb, Joanne, Park, Soo, Rubin, Gerald M, and Celniker, Susan E. A drosophila full-length cDNA resource. United States: N. p., 2003. Web.
Stapleton, Mark, Carlson, Joseph, Brokstein, Peter, Yu, Charles, Champe, Mark, George, Reed, Guarin, Hannibal, Kronmiller, Brent, Pacleb, Joanne, Park, Soo, Rubin, Gerald M, & Celniker, Susan E. A drosophila full-length cDNA resource. United States.
Stapleton, Mark, Carlson, Joseph, Brokstein, Peter, Yu, Charles, Champe, Mark, George, Reed, Guarin, Hannibal, Kronmiller, Brent, Pacleb, Joanne, Park, Soo, Rubin, Gerald M, and Celniker, Susan E. Fri . "A drosophila full-length cDNA resource". United States.
@article{osti_813593,
title = {A drosophila full-length cDNA resource},
author = {Stapleton, Mark and Carlson, Joseph and Brokstein, Peter and Yu, Charles and Champe, Mark and George, Reed and Guarin, Hannibal and Kronmiller, Brent and Pacleb, Joanne and Park, Soo and Rubin, Gerald M and Celniker, Susan E},
abstractNote = {Background: A collection of sequenced full-length cDNAs is an important resource both for functional genomics studies and for the determination of the intron-exon structure of genes. Providing this resource to the Drosophila melanogaster research community has been a long-term goal of the Berkeley Drosophila Genome Project. We have previously described the Drosophila Gene Collection (DGC), a set of putative full-length cDNAs that was produced by generating and analyzing over 250,000 expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages. Results: We have generated high-quality full-insert sequence for 8,921 clones in the DGC. We compared the sequence of these clones to the annotated Release 3 genomic sequence, and identified more than 5,300 cDNAs that contain a complete and accurate protein-coding sequence. This corresponds to at least one splice form for 40 percent of the predicted D. melanogaster genes. We also identified potential new cases of RNA editing. Conclusions: We show that comparison of cDNA sequences to a high-quality annotated genomic sequence is an effective approach to identifying and eliminating defective clones from a cDNA collection and ensure its utility for experimentation. Clones were eliminated either because they carry single nucleotide discrepancies, which most probably result from reverse transcriptase errors, or because they are truncated and contain only part of the protein-coding sequence.},
doi = {},
url = {https://www.osti.gov/biblio/813593}, journal = {Genome Biology},
number = 12,
volume = 3,
place = {United States},
year = {2003},
month = {5}
}