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Drosophila melanogaster cDNA Collections (DGC_Berkeley)

DGC_Berkeley - Drosophila melanogaster cDNA Collections

The Berkeley Drosophila Genome Project (BDGP), a consortium of the Drosophila Genome Center, has produced over 240,000 ESTs derived from various tissues. The goal of the consortium includes full-insert sequencing and assembly of non-redundant cDNA clones. Annotated sequences of all Drosophila transcripts, including products of alternative splicing, will facilitate creation of a set of Drosophila Gateway clones for use in proteomics and other functional genomics projects.

A set of ~11,000 clones has been assembled from ~90,000 EST sequences, grouped or clotted, based on sequence identity from their 5' ends. One representative from each clot was rearrayed and its 5' and 3' ends sequenced, first to verify its identity, and second to recluster on the basis of the 3' sequence.

Generation of the Release 3 annotation of the genome made extensive use of our full-insert sequence data. In the course of that effort, human curators identified a total of 1,860 clones that have become the DGCr3. The DGCr3 currently includes clones chosen to replace clones with truncated ORFs, clones for genes that are not currently represented in the DGC, plus clones that represent putative alternative splicing forms.

For more information please see BDGP webpage (http://www.fruitfly.org/DGC/index.html). We also have 3 Databases for further information, DGC 1, DGC 2 and DGC 3.

This resource is available as bacterial glycerol stocks and can be ordered as individual clones, individual 384-well plates or complete set of clones in 39 plates (DGCr1.0 = 17 plates and DGCr2.0 = 16 plates & DGCr3.0 = 6).

Protocols / Clone Handling

Plates-  contain LB broth with 8% glycerol and antibiotic*. are sent on Dry Ice. These should be stored at -70°C.
Individual clones have been streaked onto LB agar containing antibiotic*. Please store them at 4°C (not in a freezer).
As soon as possible, re-streak the clones onto the same medium and incubate overnight at 37°C to obtain single colonies.

*Antibiotic

DGCr1.0
Plates 1-4 Ampicillin 75µg/ml
Plates 5-17 Chloramphenicol 25µg/ml

DGCr2.0
Plates 1-10 Ampicillin 75µg/ml
Plates 11-16 Chloramphenicol 25µg/ml

DGCr3.0
Plates 1-3 Ampicillin 75µg/m
Plates 4-6 Chloramphenicol 25µg/ml

A selection of at least 10 single colonies should be picked and grown in LB broth containing appropriate antibiotic + 8% glycerol for subsequent freezing at -70°C. These frozen stocks can then be re-grown for plasmid isolation and purification.

Streaking out for single colonies is essential in case of contamination or cross-contamination, or if modifications of the original clone have taken place as the library has been replicated. If there is a problem, the more single colonies you streak out, the more likely it is that you can retrieve the original construct. You can also isolate the original clone from a contaminated sample by following this procedure.

References

Citation in publications

Please cite the following paper for BDGP clones or sequence data.

Mark Stapleton*†, Joe Carlson*†, Peter Brokstein*†‡, Charles Yu*†,
Mark Champe*†§ Reed George*†, Hannibal Guarin*†, Brent Kronmiller*†,
Joanne Pacleb*†, Soo Park*†, Ken Wan*†, Gerald M Rubin*¥# and
Susan E Celniker* A Drosophila full-length cDNA resource. Genome Biology,
2002;3:research0080.1-0080.8

Stapleton M, Liao G, Brokstein P, Hong L, Carninci P, Shiraki T, Hayashizaki
Y, Champe M, Pacleb J, Wan K, Yu C, Carlson J, George R, Celniker S, Rubin
GM. The Drosophila Gene Collection: Identification of Putative Full-Length
cDNAs for 70% of D. melanogaster Genes. Genome Research. 2002; 12:1294-1300.

Rubin GM, Hong L, Brokstein P, Evans-Holm M, Frise E, Stapleton M, and Harvey DA:
A Drosophila complementary DNA resource. Science 2000,
287:2222-2224.


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