Solanaceae Gene Expression Profiling

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Experiments and Data in the Solanaceae Gene Expression Database (SGED)

Our goal is to generate a comprehensive database on gene expression patterns for a wide variety of Solanaceae species.

In total, we have collaborated with 11 outside scientists per year for a total of 55 collaborators over the 5 years of the project. For these external collaborations, TIGR has received RNA from the collaborator, performed hybridizations, and entered data into the Solanaceae Gene Expression Profile Database (SGED). TIGR has provided the external collaborators with a 60 day period to analyze their data before the data is released to the public.

Data Availability

The expression data is available in several formats. The database can be queried to retrieve expression data for single clones or a list of clones. Normalized data are available for the complete studies as well. In addition, all raw data files as well as images are available for download. For details on the data processing and normalization, click here.

TIGR Solanaceae Gene Expression Profiling

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.

The TIGR Solanaceae Gene Expression Profiling Service has ended and we are no longer accepting new proposals.

TIGR Potato cDNA Microarray Description

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.

 

Last modified: Monday, 26-Jan-2009 14:33:18 EST