The objective of the research projects within this SCCOR grant proposal is to understand the molecular mechanism underlying the pathology of TOF, and to identify potential new candidate genes that play a critical role in the formation of the cardiac septa and valves, the alignment of the outflow tract, the development and function of the right ventricular chamber, and in cardiac regeneration. For this purpose, it is proposed by Projects 2, 4, 5, and 6 to perform genome-wide mRNA expression measurements on human and animal myocardial tissues that are being collected and generated within this SCCOR grant. The Microarray Core (Core B) will provide the technology, expertise, infrastructure, and resources to perform large scale expression profiling studies in order to produce high quality microarray data in the most expeditious manner. This Core will be an expansion of the CardioGenomics RNA Expression Profiling Core at Beth Israel Deaconess Medical Center (BIDMC) that was established in September 2000 as part of the NHLBI-funded Programs of Genomic Applications (PGA) (www.cardiogenomics.org). The objectives of the Microarray Core Facility are (1) to produce high quality RNA expression data and apply common standards for microarray data quality; (2) to apply and to develop software tools for data analysis that are made freely available to the scientific community; (3) to establish benchmark data sets of expression profiles for normal cardiac development and for animal models for TOF and cardiac regeneration; and (4) to establish a database of expression profiles for TOF patients. In addition to the services that are commonly provided by institutional microarray core facilities such as probe labeling, microarray hybridization, scanning, and data analysis, we will also (a) help with the experimental design to facilitate statistical analysis and to increase the significance and interpretability of the data; (b) apply vigorous quality control standards to ensure low experimental variability; (c) apply PGA nationwide established consensus standards for data collection and analysis; (d) provide centralized data management, data distribution, storage, and data backup; (e) perform customization of the data analysis strategies to meet the various goals of the projects, e.g. delineation of complex patterns of gene expression, identification of signaling pathways, functional gene annotations, identification of diagnostic markers, and hypothesis generation; and (f) perform independent data validation using real-time quantitative PCR, Northern blotting, and in situ hybridization techniques that are already well established in our laboratory. Taken together, this strategy will enable the SCCOR components to successfully apply microarray technologies in their projects. It will ensure reproducibility and high quality of the microarray data, it will facilitate the integration of data generated by the individual projects and thereby substantially increase the likelihood of success in discovering new potential candidate genes for TOF that will be subjected to mutational screening in TOF patients in Project 3.
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