Microarray Core
Director: Donald A. Baldwin, Ph.D.dbaldwin@mail.med.upenn.edu
Associate Director: John Tobias, Ph.D.
jtobias@pcbi.upenn.edu
The musculoskeletal research field is becoming increasingly focused on studies at the genetic level. In particular, a variety of evaluation tools have recently been developed that allow investigators to understand the molecular systems in which biological processes occur. The field of functional genomics seeks to annotate genomic sequences with assignments of gene and regulatory element identities and locations; RNA variants and abundance levels; and protein variants, abundances, and interactions. As functional annotations accumulate, detailed and indepth studies of specific genes and their products can be placed into a genomic context to reveal the molecular systems. In turn, those systems and processes can be studied using functional genomics techniques to identify the genes important for their regulation. One such technique is transcript profiling, the parallel quantitation of RNA abundance for thousands of genes. Transcript profiling can be open-ended, using methods that do not rely on previous knowledge of gene sequences, or closed to a defined set of probes for known RNAs. There are also ways to combine both approaches by starting with an open-ended functional enrichment of transcribed sequences and using them to create probe collections for further profiling before determining their identities.
The Penn Microarray Facility is an existing Core Facility in the School of Medicine at the University of Pennsylvania that provides instrumentation and expertise for RNA transcript profiling. The Facility primarily supports two microarray formats: 1) oligonucleotide arrays synthesized by Affymetrix, and 2) arrays of cDNAs or oligomers printed in-house on glass slides. This reflects our goal of offering a range of cost and performance options suitable for a variety of experimental questions. The overall objective of this Microarray Core Facility for our Penn Center for Musculoskeletal Disorders is to develop and utilize genomic analyses directed toward problems of musculoskeletal tissue injury and repair. The Specific Aims are:
Aim 1: To provide guidance and training on the capabilities, advantages, and disadvantages of various genomic protocols and analyses for musculoskeletal research through formal educational enrichment programs and one-on-one interactions.
Aim 2: To provide expertise and service for Affymetrix GeneChip assays.
Aim 3: To provide expertise and service for the development and use of custom printed microarrays.
Aim 4: To facilitate access to training and bioinformatics tools appropriate for analyzing the data produced in Aims 2 and 3.
Aim 5: To provide funding for development of new projects and collaborations and to facilitate development of preliminary and/or feasibility data for investigators.
Successful completion of these aims will significantly enhance the environment and the capabilities of researchers at the University of Pennsylvania, leading to novel and innovative approaches to address musculoskeletal disorders and new collaborations between Center faculty who may have not previously included microarrays in their musculoskeletal research programs.
To view Dr. Baldwin's presentation at the November 2006 Symposium Retreat click here and be patient as the file loads.
For more information, please visit Penn Microarray Facility.