Attention Tom1 Array Users

Re-sequencing of cDNAs on the TOM1 array is now complete! 

We have completed the re-sequencing and data analysis of the clones on the Tom 1 Microarray.

The clones were sequenced from both the 5' and 3' ends for us by INRA (Institut National de la Recherche Agronomique) in France and the data were deposited in the Solanaceae Genomics Network (SGN) database, located here at Cornell.

A short summary of the re-sequencing project follows:

• All the clones on the array (12,500) were submitted for re-sequencing (this represents a total of 25,000 potential sequence reactions for a 3 and 5 prime read)
• We received back a total of 19,065 raw sequences
• After removal of low quality sequences 17,066 sequences remained for analysis
• 9172 clones had new sequence information
• Out of these, 6,695 clones had sequences for both 5' and 3' ends.
• 568 clones only had 3' sequences
• 1,909 clones only had 5' sequences.
• Of the 6,695 clones with both 5' and 3' sequence, 4497 overlapped and could be assigned to the same unigene.

For an example of the detailed information you can receive from SGN for each spot click on the link below:

Example of clone info at SGN

Note: you will either see that the clone was sequenced by INRA (" Sequencing Facility: INRA" ) indicating that the clone was successfully re-sequenced or it will indicate TIGRE if we are basing our data on the original EST sequence.

http://www.sgn.cornell.edu/cgi-bin/search/est.pl?request_id=1-1-4.3.4.6&request_from=0&request_type=14

Click below to download a new array id file that has a unique spot identifier for each element on the array. These ids can be used to search the SGN database for spot information. You can also download files explaining all the different array identifiers available for each spot here at the CGEP website (click on the gene id file link on the tool bar). You can use these to customize a gene id file that best suits your particular needs.

Tom1 Array id file

CGEP encourages all array users to utilize the Tomato Expression Database which is part of the Tomato Genome Project . It includes the tomato microarray data warehouse (TMD), tomato microarray expression database (TED) and tomato digital expression database (DED).

Tomato microarray data warehouse is for public storage/retrieval of raw microarray data resulting from use of the Tom1 array. Users of Tom1 are encouraged to submit their raw data to TMD to facilitate future assessment and analyses. TMD employs the MIAME protocol for microarray experiment characterization to facilitate maximal utility for the research community. Contact the site administrator to receive a login ID and password for data submission. Below is a link to TED.

LINK TO TED