A Drosophila complementary DNA resource

Science

Volumn 287, Issue 5461, 2000, Pages 2222-2224

  Rubin, Gerald M ^a   Hong, Ling ^a   Brokstein, Peter ^a   Evans Holm, Martha ^a   Frise, Erwin ^a   Stapleton, Mark ^a   Harvey, Damon A ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; DNA; RNA;

DNA SEQUENCE; DROSOPHILA MELANOGASTER; GENE; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW;

3' UNTRANSLATED REGIONS; 5' UNTRANSLATED REGIONS; ANIMALS; CLONING, MOLECULAR; DNA, COMPLEMENTARY; DROSOPHILA MELANOGASTER; EXPRESSED SEQUENCE TAGS; GENE LIBRARY; GENES, INSECT; OPEN READING FRAMES;

DROSOPHILA MELANOGASTER; MELANOGASTER;

EID: 0034708827     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.287.5461.2222     Document Type: Review

References (15)

1. R. L. Strausberg, E. A. Feingold, R. D. Klausner, F. S. Collins, Science 286, 455 (1999).
2. Total RNA was prepared by hot phenol extraction. mRNA was purified with the Stratagene Poly(A) Quik mRNA isolation kit. mRNA quality was assessed by RNA blots with Delta and Notch clones as probes. First strand cDNA synthesis was carried out with the Stratagene λZAPII-cDNA synthesis kit with the substitution of Superscriptll reverse transcriptase from GIBCO-BRL. The cDNAs were directionally cloned into the λZAPII and pOT2a vectors. Phage and plasmid libraries were amplified once. The plasmid libraries were size fractionated with GIBCO-BRL S-500 cDNA size fractionation columns, and clones with inserts larger than 1 kb were pooled and transformed.
3. M. F. Bonaldo, G. Lennon, M. B. Soares, Genome Res. 6, 791 (1996).
4. M. D. Adams et al., Science 252, 1651 (1991).
5. 5' ESTs were generated with either dye primer or dye terminator chemistries on ABI373 and ABI377 sequencers.
6. M. D. Adams et al., Science 287, 2185 (2000).
7. Clustering was done by first collecting similar sequences with BLAST and then aligning these sequences with PHRAP. Details of the computational methods used in this work will be described elsewhere.
8. 3' ESTs were generated on an ABI377 sequencer with rhodamine dye terminators or by dye primer sequencing on a Licor sequencer.
9. Alignments were performed with SIM4.
10. The length of the cDNA insert was determined by PCR amplification with vector primers that flank the cloning sites, and the products were sized by agarose gel electrophoresis.
11. The individual clones corresponding to all 80,000 of our ESTs are available through Research Genetics, including all clones that are in the DGC set. We anticipate that the DGC as a separate collection of cDNAs will be available for distribution in May 2000.
12. D. J. Monroe et al., Proc. Natl. Acad. Sci. U.S.A. 92, 2209 (1995).
13. X. Huang and W. Miller, Adv. Appl. Math. 12, 373 (1991).
14. L. D. Hillier et al., Genome Res. 6, 807 (1996).
15. The following individuals helped generate the sequence data reported here: E. Baxter, R. Blazej, M. Chew, C. Doyle, R. Galle, R. George, R. Hoskins, D. Kruse, J. Landau, H. Meagher, A. Pinder, S. Richards, C. Suh, G. Tsang, and C. Yu. We are especially grateful to S. Lewis for her help in developing the informatics tools used to support this work, K. Wan and M. Champe for their technical contributions to the sequencing, and S. Celniker for her management of the Lawrence Berkeley National Laboratory sequencing facility in which some of this work was done. A. Spradling provided the RNA used to construct the GM library. C. Nelson and A. Huang helped improve the writing. The generation of the 5' ESTs was supported by the Howard Hughes Medical Institute. Other aspects of this work were supported by grant DE-FG03-98ER62625 from the Department of Energy.