Genome Research cityscape

Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
 QUICK SEARCH:   [advanced]


     


This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Stapleton, M.
Right arrow Articles by Rubin, G. M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Stapleton, M.
Right arrow Articles by Rubin, G. M.
Social Bookmarking
 Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Vol. 12, Issue 8, 1294-1300, August 2002

RESOURCES
The Drosophila Gene Collection: Identification of Putative Full-Length cDNAs for 70% of D. melanogaster Genes

Mark Stapleton,1,2,6 Guochun Liao,1,3 Peter Brokstein,1,3 Ling Hong,1,3 Piero Carninci,4 Toshiyuki Shiraki,4 Yoshihide Hayashizaki,4 Mark Champe,1,2 Joanne Pacleb,1,2 Ken Wan,1,2 Charles Yu,1,2 Joe Carlson,1,2 Reed George,1,2 Susan Celniker,1,2 and Gerald M. Rubin1,3,5

1 Berkeley Drosophila Genome Project, 2 Genome Sciences Department, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; 3 Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3200, USA; 4  Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; 5 Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA

Collections of full-length nonredundant cDNA clones are critical reagents for functional genomics. The first step toward these resources is the generation and single-pass sequencing of cDNA libraries that contain a high proportion of full-length clones. The first release of the Drosophila Gene Collection Release 1 (DGCr1) was produced from six libraries representing various tissues, developmental stages, and the cultured S2 cell line. Nearly 80,000 random 5' expressed sequence tags (5' expressed sequence tags [ESTs]from these libraries were collapsed into a nonredundant set of 5849 cDNAs, corresponding to ~40% of the 13,474 predicted genes in Drosophila. To obtain cDNA clones representing the remaining genes, we have generated an additional 157,835 5' ESTs from two previously existing and three new libraries. One new library is derived from adult testis, a tissue we previously did not exploit for gene discovery; two new cap-trapped normalized libraries are derived from 0-22-h embryos and adult heads. Taking advantage of the annotated D. melanogaster genome sequence, we clustered the ESTs by aligning them to the genome. Clusters that overlap genes not already represented by cDNA clones in the DGCr1 were analyzed further, and putative full-length clones were selected for inclusion in the new DGC. This second release of the DGC (DGCr2) contains 5061 additional clones, extending the collection to 10,910 cDNAs representing >70% of the predicted genes in Drosophila.

[The sequence data described in this paper have been submitted to the GenBank data library under accession nos. BF485518-BF503517, BF503521-BF506780, BG631888-BG631996, BG633696-BG637540, BG640063-BG641469, BI141709-BI142246, BI161485-BI173971, BI212109-BI216987, BI227448-BI233322, BI234009-BI243989, BI351612-BI354228, BI354231-BI355901, BI355935-BI358751, BI361285-BI376197, BI481532-BI487261, BI563331-BI593695, BI604243-BI620155, BI620158-BI635012, BI635064-BI638027, and BI638030-BI642053. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: J. Pringle and M. Fuller.]


6 Corresponding author.


12:1294-1300 ©2002 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/02 $5.00

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
Genome Res.Home page
M. F. Lin, J. W. Carlson, M. A. Crosby, B. B. Matthews, C. Yu, S. Park, K. H. Wan, A. J. Schroeder, L. S. Gramates, S. E. St. Pierre, et al.
Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes
Genome Res., December 1, 2007; 17(12): 1823 - 1836.
[Abstract] [Full Text] [PDF]


Home page
J. Cell Sci.Home page
A. V. Pindyurin, C. Moorman, E. de Wit, S. N. Belyakin, E. S. Belyaeva, G. K. Christophides, F. C. Kafatos, B. van Steensel, and I. F. Zhimulev
SUUR joins separate subsets of PcG, HP1 and B-type lamin targets in Drosophila
J. Cell Sci., July 15, 2007; 120(14): 2344 - 2351.
[Abstract] [Full Text] [PDF]


Home page
ScienceHome page
R. A. Hoskins, J. W. Carlson, C. Kennedy, D. Acevedo, M. Evans-Holm, E. Frise, K. H. Wan, S. Park, M. Mendez-Lago, F. Rossi, et al.
Sequence Finishing and Mapping of Drosophila melanogaster Heterochromatin
Science, June 15, 2007; 316(5831): 1625 - 1628.
[Abstract] [Full Text] [PDF]


Home page
RNAHome page
M. Stapleton, J. W. Carlson, and S. E. Celniker
RNA editing in Drosophila melanogaster: New targets and functional consequences
RNA, November 1, 2006; 12(11): 1922 - 1932.
[Abstract] [Full Text] [PDF]


Home page
Genes Dev.Home page
G. Legube, S. K. McWeeney, M. J. Lercher, and A. Akhtar
X-chromosome-wide profiling of MSL-1 distribution and dosage compensation in Drosophila
Genes & Dev., April 1, 2006; 20(7): 871 - 883.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
C. D. Schmid, R. Perier, V. Praz, and P. Bucher
EPD in its twentieth year: towards complete promoter coverage of selected model organisms
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D82 - D85.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
R. A. Hoskins, M. Stapleton, R. A. George, C. Yu, K. H. Wan, J. W. Carlson, and S. E. Celniker
Rapid and efficient cDNA library screening by self-ligation of inverse PCR products (SLIP)
Nucleic Acids Res., December 2, 2005; 33(21): e185 - e185.
[Abstract] [Full Text] [PDF]


Home page
Genome Res.Home page
M. Ashburner and C. M. Bergman
Drosophila melanogaster: A case study of a model genomic sequence and its consequences
Genome Res., December 1, 2005; 15(12): 1661 - 1667.
[Abstract] [Full Text] [PDF]


Home page
GENES CELLSHome page
S. Inagaki, K. Numata, T. Kondo, M. Tomita, K. Yasuda, A. Kanai, and Y. Kageyama
Identification and expression analysis of putative mRNA-like non-coding RNA in Drosophila
Genes Cells, December 1, 2005; 10(12): 1163 - 1173.
[Abstract] [Full Text] [PDF]


Home page
J. Cell Biol.Home page
C. D'Alterio, D. D.D. Tran, M. W.Y. A. Yeung, M. S.H. Hwang, M. A. Li, C. J. Arana, V. K. Mulligan, M. Kubesh, P. Sharma, M. Chase, et al.
Drosophila melanogaster Cad99C, the orthologue of human Usher cadherin PCDH15, regulates the length of microvilli
J. Cell Biol., November 7, 2005; 171(3): 549 - 558.
[Abstract] [Full Text] [PDF]


Home page
Mol. Biol. CellHome page
J. K. Jang, T. Rahman, and K. S. McKim
The Kinesinlike Protein Subito Contributes to Central Spindle Assembly and Organization of the Meiotic Spindle in Drosophila Oocytes
Mol. Biol. Cell, October 1, 2005; 16(10): 4684 - 4694.
[Abstract] [Full Text] [PDF]


Home page
RNAHome page
S. LEE, J. BAO, G. ZHOU, J. SHAPIRO, J. XU, R. Z. SHI, X. LU, T. CLARK, D. JOHNSON, Y. C. KIM, et al.
Detecting novel low-abundant transcripts in Drosophila
RNA, June 1, 2005; 11(6): 939 - 946.
[Abstract] [Full Text] [PDF]


Home page
Mol. Biol. CellHome page
Y. Guo, S. Jangi, and M. A. Welte
Organelle-specific Control of Intracellular Transport: Distinctly Targeted Isoforms of the Regulator Klar
Mol. Biol. Cell, March 1, 2005; 16(3): 1406 - 1416.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
M. Yandell, A. M. Bailey, S. Misra, S. Shu, C. Wiel, M. Evans-Holm, S. E. Celniker, and G. M. Rubin
A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome
PNAS, February 1, 2005; 102(5): 1566 - 1571.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
J. Kuo, J. Inman, M. Brownstein, and T. B. Usdin
Evaluation of vector-primed cDNA library production from microgram quantities of total RNA
Nucleic Acids Res., December 15, 2004; 32(22): e183 - e183.
[Abstract] [Full Text] [PDF]


Home page
Plant Cell PhysiolHome page
T. Nanjo, N. Futamura, M. Nishiguchi, T. Igasaki, K. Shinozaki, and K. Shinohara
Characterization of Full-length Enriched Expressed Sequence Tags of Stress-treated Poplar Leaves
Plant Cell Physiol., December 15, 2004; 45(12): 1738 - 1748.
[Abstract] [Full Text] [PDF]


Home page
cellbioedHome page
M. Rice, W. Gladstone, and M. Weir
Relational Databases: A Transparent Framework for Encouraging Biology Students To Think Informatically
CBE Life Sci Educ, December 1, 2004; 3(4): 241 - 252.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
T. Raabe, S. Clemens-Richter, T. Twardzik, A. Ebert, G. Gramlich, and M. Heisenberg
Identification of Mushroom body miniature, a zinc-finger protein implicated in brain development of Drosophila
PNAS, September 28, 2004; 101(39): 14276 - 14281.
[Abstract] [Full Text] [PDF]


Home page
Genome Res.Home page
T. E. Scheetz, J. J. Laffin, B. Berger, S. Holte, S. A. Baumes, R. Brown II, S. Chang, J. Coco, J. Conklin, K. Crouch, et al.
High-Throughput Gene Discovery in the Rat
Genome Res., April 1, 2004; 14(4): 733 - 741.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
D. R. Herr, H. Fyrst, M. B. Creason, V. H. Phan, J. D. Saba, and G. L. Harris
Characterization of the Drosophila Sphingosine Kinases and Requirement for Sk2 in Normal Reproductive Function
J. Biol. Chem., March 26, 2004; 279(13): 12685 - 12694.
[Abstract] [Full Text] [PDF]


Home page
Genome Res.Home page
M. Weir and M. Rice
Ordered Partitioning Reveals Extended Splice-Site Consensus Information
Genome Res., January 1, 2004; 14(1): 67 - 78.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
C. D. Schmid, V. Praz, M. Delorenzi, R. Perier, and P. Bucher
The Eukaryotic Promoter Database EPD: the impact of in silico primer extension
Nucleic Acids Res., January 1, 2004; 32(90001): D82 - 85.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
K. Mita, M. Morimyo, K. Okano, Y. Koike, J. Nohata, H. Kawasaki, K. Kadono-Okuda, K. Yamamoto, M. G. Suzuki, T. Shimada, et al.
The construction of an EST database for Bombyx mori and its application
PNAS, November 25, 2003; 100(24): 14121 - 14126.
[Abstract] [Full Text] [PDF]


Home page
Genes Dev.Home page
F. Greil, I. van der Kraan, J. Delrow, J. F. Smothers, E. de Wit, H. J. Bussemaker, R. van Driel, S. Henikoff, and B. van Steensel
Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location
Genes & Dev., November 15, 2003; 17(22): 2825 - 2838.
[Abstract] [Full Text] [PDF]


Home page
Genome Res.Home page
M. Labrador and V. G. Corces
Extensive Exon Reshuffling Over Evolutionary Time Coupled to Trans-Splicing in Drosophila
Genome Res., October 1, 2003; 13(10): 2220 - 2228.
[Abstract] [Full Text] [PDF]


Home page
Sci SignalHome page
A. M. Michelson
Running Interference for Hedgehog Signaling
Sci. Signal., July 22, 2003; 2003(192): pe30 - pe30.
[Abstract] [Full Text] [PDF]


Home page
Genome Res.Home page
O. Jaillon, C. Dossat, R. Eckenberg, K. Eiglmeier, B. Segurens, J.-M. Aury, C. W. Roth, C. Scarpelli, P. T. Brey, J. Weissenbach, et al.
Assessing the Drosophila melanogaster and Anopheles gambiae Genome Annotations Using Genome-Wide Sequence Comparisons
Genome Res., July 1, 2003; 13(7): 1595 - 1599.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
T. Nishiyama, T. Fujita, T. Shin-I, M. Seki, H. Nishide, I. Uchiyama, A. Kamiya, P. Carninci, Y. Hayashizaki, K. Shinozaki, et al.
Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: Implication for land plant evolution
PNAS, June 24, 2003; 100(13): 8007 - 8012.
[Abstract] [Full Text] [PDF]


Home page
Genome Res.Home page
E. D. Pleasance, M. A. Marra, and S. J.M. Jones
Assessment of SAGE in Transcript Identification
Genome Res., June 1, 2003; 13(6): 1203 - 1215.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
J. A. Sellers, L. Hou, H. Athar, M. M. Hussain, and G. S. Shelness
A Drosophila Microsomal Triglyceride Transfer Protein Homolog Promotes the Assembly and Secretion of Human Apolipoprotein B: IMPLICATIONS FOR HUMAN AND INSECT LIPID TRANSPORT AND METABOLISM
J. Biol. Chem., May 23, 2003; 278(22): 20367 - 20373.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
G. Yuan, C. Klambt, J.-P. Bachellerie, J. Brosius, and A. Huttenhofer
RNomics in Drosophila melanogaster: identification of 66 candidates for novel non-messenger RNAs
Nucleic Acids Res., May 15, 2003; 31(10): 2495 - 2507.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
A. G. Saez, A. Tatarenkov, E. Barrio, N. H. Becerra, and F. J. Ayala
Patterns of DNA sequence polymorphism at Sod vicinities in Drosophila melanogaster: Unraveling the footprint of a recent selective sweep
PNAS, February 18, 2003; 100(4): 1793 - 1798.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
The FlyBase database of the Drosophila genome projects and community literature
Nucleic Acids Res., January 1, 2003; 31(1): 172 - 175.
[Abstract] [Full Text] [PDF]




Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
Genes Dev. Learn. Mem.
Protein Science RNA Genome Res.