Drosophila Genomics Resource Center Justen Andrews Peter Cherbas http://dgrc.cgb.indiana.edu/
Drosophila Genomics Resource Center • Clones/vectors/RNAi/2-hybrid • collection ~300,000, distribution >3,000 • Cell lines • collection ~ 100, distribution >200 • Microarrays • Amplcon transcriptome microarrays, distributed ~500 • Oligonucleotide transcriptome microarrays (INDAC) pending • Distribuion of genome tiling microarrays (White Russell) pending • Users • Individual: total 1,500, active 600 • Laboratory: total 650, active 500
Amplicon transcriptome arrays • Comprehensive amplicon microarrays • Probes PCR amplified using gene specific primers • Donated by Incyte Genomics and Brian Oliver, NIDDK • 15,552 spots = 10,000 non-redundent r3.1 genes • Quality control: gels, stain, barcode, hybridization • Shipped ready for hybridization • Gene lists, QC data and protocols available for download at web site
Systematic functional annotation of the transcriptome: the big picture Where are all the transcription units, what are all the splice variants, in which cells are they expressed? Where are all the cis-regulatory sequences, what are the corresponding trans-factors, what is the regulatory network diagram through space and time? The solution is going to include a range of integrated experimental and computational approaches (comparative sequence analysis, transcriptional profiling, chip-chip) spanning a range of organizational levels (centers, consortia, individual labs).
Resolution will increase over time resolution: high low genome tiling path microarrays: gene specific transcript specific species specific animals organs tissue: cell types genetic background organization: decentralized centralized
Issues • Microarray resources will evolve as our knowledge base increases • oligonucleotide probes against current gene models will be relatively stable • microarray evolution should be by addition rather than by revolution so that data is back compatible, eg gene specific -> exon/splice specific • INDAC oligonucleotide arrays serve as a useful starting point for future versions: exon specific, to be used internationally • will it be possible to develop a Drosophila pan-species transcriptome microarray(s)?
Issues • Isolation of cell types is an immediate technical challenge • Dissection, LCM, FACS • New technologies • Is a facility efficient/logical?
Issues • Integration between systematic centralized and de-centralized approaches • Overall efficiency will be maximized if all units use common reagents with compatible data • Data standards and data warehousing/mining should be coordinated • Should be addressed at the planning stage
Issues • Resource distribution • Specific plan now required by NIH • Should be addressed at the planning stage
DONORS Incyte Genomics Brian Oliver NIDDK Illumina BDGP CuraGen Walter Gehring Mitsubishi Institute Pat O’Farrell Others GRANT SUPPORT NCRR NIGMS DGRC Peter Cherbas Thom Kaufman Kris Klueg Lucy Cherbas Jennifer Steinbachs Chris Hemerich Sally Todd ADVISORY BOARD Ken Burtis Reed George Alex Lash Brian Oliver Susan Parkhurst J Tim Westwood Kevin White