Sexdetermination

1
Drosophila Genomics Resource Center
Justen Andrews Peter Cherbas http//dgrc.cgb.in
diana.edu/
2
Drosophila Genomics Resource Center

• Clones/vectors/RNAi/2-hybrid
• collection 300,000, distribution gt3,000
• Cell lines
• collection 100, distribution gt200
• 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

3
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

4
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).
5
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
6

• 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 -gt 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)?

7

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

8

• 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

9

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

10
DONORS Incyte Genomics Brian Oliver NIDDK Illumina
BDGP CuraGen Walter Gehring Mitsubishi
Institute Pat OFarrell 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