The primary goal of Core B will be to provide access to complementary transcriptional profiling technologies to examine differential mRNA expression during tolerance induction and rejection in different model systems studied by the individual projects. The main objectives of the core will be to consult and train on functional genomics and bioinformatics, to provide standardized methods for quality control and validation of microarray experiments, to offer experienced onsite staff to perform microarray experiments and to analyze the data, to implement, update, and develop bioinformatics and biostatistics software tools for microarray analysis and data mining, and to develop a standardized database and interactive research portal. The core will label the cDNA or cRNA probes, hybridize customized and commercial arrays as well as provide a comprehensive analysis of the microarray data using biostatistical and bioinformatic software tools. Data generated by the core will be uploaded to the Research Portal and incorporated into a database for further analysis and querying by the individual investigators for hypothesis generation. The Core will establish the Immune Tolerance Research Portal (ITRP) to provide webaccessible data entry, annotation, cataloging facilities and state-of -the-art bioinformatics analyses. In addition, the core will develop new bioinformatics tools for data analysis and integration of metadata with the aim to build biological pathways. This will enable researchers from all Projects to maximally utilize the expression data sets to determine functional dependencies among the known genes and Expressed Sequence Tags (ESTs) and direct further biological validation of these putative dependencies. The facility will use two complementary microarray methodologies. Affymetrix GeneChip arrays of murine expressed sequences and customized focused microarrays on glass slides spotted with long oligonucleotides encoding immunologically relevant genes.
The specific aims are:
Aim 1 : Establish a webaccessible Immune Tolerance Research Portal (ITRP) for data entry and analysis.
Aim 2 : Standardized RNA expression data from biological samples obtained from the individual Projects.
Aim 3 : Develop """"""""noise-aware"""""""" Benchmark Data Sets (BDS) for normal murine tissues and cells.
Aim 4 : Hypothesis Generation: Use bioinformatics techniques to identify functional dependencies. By providing these services as a core function, we aim to save time and money and to establish quality controls and standardized procedures and reagents, which will lead to standardized data sets that can be compared and shared by different investigators in the program. In addition, integration of data sets from the different projects may by itself generate new insights not visible in individual data sets.
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