MICROARRAY ANALYSIS CORE

The Microarray Analysis Core (MAC) of the Rochester Nathan Shock Center for Excellence in Aging Research announces the second quarterly call for research proposals that will subsidize the use of an Affymetrix gene expression study relevant to aging research.

This mechanism of support will provide a 100% subsidy on the processing of 8 samples using the URMC Microarray Core. Currently the cost of processing a sample is $700 . This subsidy provides free processing for up to 4 replicates with one experimental variable for obtaining gene expression data. Consultation with the Director of the MAC (Dr. David Pearce) is strongly advised before submitting a proposal.

The proposal should be brief, not more than one page, outlining an experiment that utilizes Affymetrix gene chips. Please note that the awardee is expected to cover the cost of the Affymetrix chips.

Proposals will be reviewed for their applicability to aging research, and the potential for successfully gaining insight into the process under investigation. Investigators who have not utilized Microarray technology before or are looking to initiate research on an aging related topic are encouraged to apply. Proposals should be submitted to Dr. David Pearce, via email (David_Pearce@urmc.rochester.edu). Hard copies (2 copies) may be submitted to Dr. Pearce at Box 645. Deadline for receipt is October 15, with anticipated award date of October 30.

Aims:

• The Microarray Analysis Core (MAC) advances aging-related research by providing state-of-the-art gene profiling from multiple tissue or cell types using DNA microarrays.
• The MAC also provides basic data analyses for all array experiments.

Introduction:

Predictions relating to cellular function in aging organ systems can be directly correlated to gene expression. Profiling expression levels from organ systems, specific anatomical locations and even from single cells is of paramount importance to aging related research. Measuring the expression levels of large numbers of genes in a traditional manner is an arduous process that consumes a great deal of time, reagents and biological material. The development of high-density expression arrays has made it possible to simultaneously screen small amounts of biological samples for thousands of genes. The Rochester Nathan Shock Center supports a state-of-the-art microarray facility that enables all core users to access and screen commercially available high density expression arrays, as well as, custom arrays to advance aging related research. Expression profiles generated by Microarray Analysis Core (MAC) core users helps form a database for Nathan Shock investigators. Available equipment that comprise the MAC include the Affymetrix GeneChip system and GeneChip bioinformatics system. The GeneChip system includes all of the hardware necessary for running and analyzing high-density oligonucleotide arrays for human, mouse, rat and yeast. The GeneChip bioinformatics system includes a complete laboratory information management system (LIMS) and Expression Data Mining Tool (EDMT) that allows MAC users to manage data and track projects by organizing and relating various types of data. In addition to cataloging sample details, process information, raw intensities of scanned arrays and analyzed results, the LIMS works in conjunction with the EDMT, allowing MAC users to acquire, analyze and query gene expresison data in an expedient and efficient manner. All GeneChip runs are automatically uploaded to the LIMS and made available for relational comparison with data from other investigators. Users work with the MAC to provide RNA suitable for target generation. Finally, the MAC offers a gene expression validation service that works in conjunction with the Molecular and Cellular Imaging and Gene Expression Cores. TaqMan chemistry is employed to assess gene expression via real-time RT-PCR (Perkin Elmer 7700). A set of five housekeeping gene primer and probe pairs (for both human and murine samples) including, GAPDH, beta-actin, transferrin receptor, cyclophilin, and elongaton factor 1-alpha are made available to all MAC users to aid in validation of array data. Data analysis is provided in two formats. First, a basic gene expression analysis that depicts "fold change" is supplied by the MAC upon completion of the experiment. Secondly, more detailed analysis is provided at the user-defined workstation through the EDMT.

Facilities and Services:

The MAC provides the following services:

• State-of-the-art gene profiling and analysis via microarrays for multiple tissue types including regional and single cell analysis.
• Basic data analysis for GeneChip and custom array experiments. More detailed and custom analysis is performed in a collaborative effort with the Bioinformatics and Biostatistics Core.
• cDNA synthesis, cRNA labeling, target hybridization, probe array washing and staining, probe array scanning, and data analysis.
• Database development in conjunction with the Bioninformatics and Biostatistics Core containing all experimental data generated by the MAC which is made available for relational comparisons between studies conducted.
• Real-time quantitative RT-PCR services in conjunction with the Gene Expression Vector Core to validate microarray data.