Texas A&M University Shared Instrumentation Facility

Functional Genomics Lab (Dr. Terry Thomas, Director)

The goal of the Functional Genomics Lab is to provide all investigators access to state-of-the-art functional genomics and bioinformatics resources. The specific aims of the core are to:

Facilitate investigator efforts to obtain or develop unigene sets for construction of relevant DNA microarrays.
Construct DNA microarrays that will facilitate Shared Instrumentation Facility objectives.
Coordinate multi-platform gene expression experiments of users.
Compile, display and archive expression data.
Acquire or develop new technologies to advance global gene expression analysis capabilities. This includes developing and comparing alternative and new transcriptional profiling platforms.

The Functional Genomics Lab has directly facilitated the genomics activities for the Shared Instrumentation Facility. These activities have specifically focused on cDNA library construction and curation, EST sequencing and development and analysis of DNA microarrays.

In collaboration with researchers of P01 Project 4 (PI: Cassone), cDNA libraries were constructed from chick pineal following entrainment by constant light or darkness. We have sequenced 11,904 cDNAs from the day and the night pineal libraries. We have developed a robust and rigorous sequence analysis pipeline that facilitated contig assembly and ultimately will lead to the development of a chick pineal unigene set for microarray analysis. In the meantime, we constructed a DNA microarray including 7,988 of the sequenced day and night pineal cDNAs. This microarray was used to conduct an extensive gene expression analysis of the chick pineal in P01 Project 4.

Working with researchers of P01 Project 2 (PI: Earnest), Stratagene's Lambda Zap CMV Vector Kit was used to construct two libraries; 10,000 cDNA clones from each library were picked using the Qbot (Genetix) and arrayed into 384 well microtiter plates. So far, 6,816 cDNAs have been sequenced from the Rat SCN2.2 libraries. EST sequencing and analysis is ongoing. A DNA microarray containing more than 6,000 SCN genes has been constructed, and transcriptional profiling experiments are being initiated. Affymetrix gene chip experiments have also been conducted.

The Functional Genomics Lab has also provided the technology platform for P01 Project 3, "Analysis of Circadian Output Pathways in Fungi." This project has been very productive and has resulted in the first microarray experiment published for Neurospora .

The Functional Genomics Lab awaits completion of the Synechococcus genome before initiating DNA microarray production and analysis. Significant progress has been made on the sequencing project, and it is anticipated that cyanobacterial gene sequences will be available in the near future to fabricate DNA microarrays.