Targets of Discovery

The goal of the TREX PGA is an analysis of rodent models of heart, lung, blood, and sleep disorders. We have begun our studies in the following areas and anticipate having data available in the near future.

Mouse

1. We are generating an expression encyclopedia representing expressed sequences in nine different tissues, representing both sexes in each of three strains, DBA/2, C57BL/6, and A/J:

Tissue Tissue Tissue

Liver Kidney Aorta

Lung Brain stem Intestine

Heart Upper Brain Reticulocytes

Our first target for expression profiling will be upper brain (cortex), followed by brain stem, with other tissues to be selected based on available phenotypes.

2. Innate Immunity can be assayed by studying immune response to pathogen challenge, or modeled using response to stimulation by Lipo-polysaccharides (LPS). We are currently collecting RNA samples from mouse mutants known to be either high or low responders to LPS challenge, as well as the parental strains.

3. Sleep disorders are thought to involve disruption of Circadian regulated genes. We will soon begin RNA collection from mice during a full circadian cycle and use these to assay temporal patterns of gene expression. phenotyping protocols: Prolonged Wakefulness Intermittent Hypoxia

Rat

1. There has been an increased interest in using oligos for microarray experiments both within and outside the PGA. To test the utility of printed oligo arrays, we are performing a systematic analysis of 70-mer rat oligos and corresponding sequence verified cDNA clones. The goal of this study is to provide detailed protocols describing optimized printing concentrations of non-derivatized oligos, cross-linking strategies of oligos, ideal hybridization conditions for Cy-labeled probes and oligos, and direct comparison of expression data from oligo and cDNA arrays.

2. The overall goal of the Rat Gene Expression Anatomy Project is to generate microarray expression data for rat models of heart, lung, blood, and sleep disorders. We proposed to examine both parental and chromosomal substitution (consomic) strains developed at PhysGen in order to identify patterns of gene expression and to associate these patterns with disease phenotypes. PhysGen is currently collecting RNA samples and phenotypic data from SS.BN and FHH.BN consomic panels. A subset of animals have been subjected to hypoxia conditioning for 2 weeks. Gene expression profiles from four tissues (lung, heart, kidney and liver) and two environmental conditions (normoxia, 21% O₂ and hypoxia, 12% O₂) from each strain will be collected. Transcriptomic profiles from both male and female animals will be generated. All transcriptomic data will be deposited at ArrayExpress.