TIGR Solanaceae Gene Expression Profiling Service

To increase the available data on the Solanaceae, TIGR has established a gene expression profiling service for the Solanaceae community. TIGR has established a proposal solicitation mechanism in which community researchers provide mRNA samples for a series of hybridization experiments they wish to have performed through our service. TIGR will label and hybridize the RNA submitted by the collaborator. The NSF Potato Functional Genomics Project: Application to Analysis of Growth, Development, Metabolism and Responses to Biotic and Abiotic Stress, provides resources to work with 11 scientists per year, for a total of 55 scientists throughout the project period.

Solanaceae cDNA (EST) Microarrays

TIGR has constructed spotted microarrays that contain approximately ~12,000 potato clones from ESTs that have been re-sequenced and validated. Although all clones on the microarray are from potato (Solanum tuberosum) samples from other Solanaceae species such as tomato, tobacco, petunia, eggplant and Nicotiana benthamiana can be successfully hybridized to the microarrays due to the high level of sequence similarity among the Solanaceae.

Research Proposals

Researchers are encouraged to submit a proposal for a microarray experiment relevant to the biology of any member of the Solanaceae family. The maximum number of slides per proposal is 30. To generate useful data for the user and the public, the proposal should have at least two biological replicates but three biological replicates are preferred.

The microarray experiments and data analysis will be performed at TIGR. All the user has to do is send the RNA to TIGR. The user will receive all data from the experiment from TIGR. The user will not be charged any fees for these services except for the cost of shipping the samples to TIGR.

Data Release Policy

All expression data from the expression profiling service will be made public after 60 days via the TIGR Solanaceae Gene Expression Profile database. The external collaborators will have their data exclusively for the first 60 days after they have received the expression data from TIGR.

Application Procedure

Note: the Expression Profiling Service program has ended and we are no longer accepting any new applications for this service.

Applications should be in the following format and should not exceed four (4) pages total. The application form can be found here (pdf, 19.4k).

All research conducted as part the NSF Functional Genomics Project will be subject to the data release policies of the project as described above, therefore, all applications must be signed by the applicant as well an official authorized to sign for the applicant's home institution. Therefore, the proposal needs to be faxed to TIGR or be in pdf format containing the signatures. Applications received will be reviewed typically within a month after the deadline for each round. Applications will be judged on scientific merit, feasibility, impact of the research and general interest of the data from the experiment. Due to the limitation of resources available at TIGR, only a limited number of proposals can be selected each round. Applicants whose proposals are rejected are encouraged to resubmit their proposal for the next round. After acceptance of the proposal the collaborators will receive detailed instructions from TIGR. The collaborators have to comply with these instructions and provide all the information about their experiments to TIGR.

Application Guidelines

The maximum number of slides per proposal is 30. There should be at least one independent biological replicate and preferably two. A biological replicate should be an independent repetition of the experiment and not an independent RNA isolation of the same biological sample. TIGR requires 120 ug of total RNA per hybridization. It should be taken in account whether it is feasible to isolate this amount of RNA when designing the experiments. If the same control RNA is used for multiple slides that amount of RNA should be sent. Alternatively, amplified RNA can be used.

The RNA samples must be available to TIGR within 6 months after acceptance of the proposal. It is the user's responsibility to cover all charges including, but not limited to, shipping, custom fees, duties and taxes, related to sending your RNA to TIGR. It is the user's responsibility to confirm with and pay the shipping company for any and all expenses related to shipping, custom fees, taxes and/or duties placed on your shipment. If TIGR is invoiced the users shipping company for any custom fees, duties and/or taxes outstanding that related to your shipment, TIGR will invoice the user for these charges. In addition, your samples will not be tested until payment is received by TIGR. TIGR accepts no liability or responsibility for any shipments.

Application Deadlines

• October 1 2005 - RNA samples should be sent to TIGR before May 1 2006.
• March 1 2006 - RNA samples should be sent to TIGR before October 1 2006.
• October 1 2006 - RNA samples should be sent to TIGR before May 1 2007.