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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

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slide1

Drosophila Genomics Resource Center

Justen Andrews

Peter Cherbas

http://dgrc.cgb.indiana.edu/

slide2

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
slide3

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
slide4

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).

slide5

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

slide6

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)?
slide7

Issues

  • Isolation of cell types is an immediate technical challenge
    • Dissection, LCM, FACS
    • New technologies
    • Is a facility efficient/logical?
slide8

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
slide9

Issues

  • Resource distribution
    • Specific plan now required by NIH
    • Should be addressed at the planning stage
slide10

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