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Available tomato microarray platforms

Available tomato microarray platforms. Tom1: cDNA spotted array; 12K spots; 8K unigenes; Developed at Cornell University. Publicly available. Tom2: Long oligo spotted array; 12K spots; 11K unigenes; International collaboration. Includes all Tom1 unigenes. Publicly available.

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Available tomato microarray platforms

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  1. Available tomato microarray platforms Tom1: cDNA spotted array; 12K spots; 8K unigenes; Developed at Cornell University. Publicly available. Tom2: Long oligo spotted array; 12K spots; 11K unigenes; International collaboration. Includes all Tom1 unigenes. Publicly available. Affy public microarray: 10K probe sets; 9K unigenes; Company-developed; Publicly available. <30% overlap with Tom2. Affy-Syngenta microarray: 23K unigenes; Company-developed; Proprietary. Custom platforms: Nimblegen, Agilent, Combimatrix. There is a need for a comprehensive, widely used, reasonably priced tomato transcriptional profiling platform

  2. Databases: TIGR/Dana Farber, MicroBASE, SGN, TomatEST 250K ESTs, 18K TCs + 28K singletons = 46K Unigenes Projected number of tomato genes = 35-38K Covered non-redundant transcriptome: 28 Mb Projected transcriptome length = 100-125 Mb The tomato transcriptome Efforts under way: Developmental stage-specific 454 cDNA sequencing  More extensive coverage, assembly of singletons Full-length cDNA sequencing  More complete 5’ coverage, assembly of singletons IL-specific 454 cDNA sequencing  More complete 3’ coverage, SNPs and their mapping to S. lycopersicum x S. pennelli bins SAGE, Solexa  miRNA sequences

  3. Affy chip Affy’s proposal: 1 M probes (and mismatch probes) Full transcript, custom design A minimum of 540 microarrays ordered Our desires: Publicly available array Coverage of all available unigenes Upgradability at no cost as genome sequence progresses Possible bonus features: miRNA probes, antisense probes, probes for validation of gene models, SNP mapping

  4. Allow grace period for data submitted to the database before they go public How to do it 454 sequencing Solexa sequencing Full-length cDNAs Gene models ESTs Expression database Chip design Chip fabrication and validation Chip distribution By September 2007

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