Microarray Core Facility Description


Office: 277 John Morgan Bldg.
Lab: 68 John Morgan Bldg.

Staff and Telephone numbers:

Facility Director: Don A. Baldwin, Ph.D.
Fax: 898-4227
Email: dbaldwin {at} mail.med.upenn.edu

Research Specialists:

Grace Straszewski, Jennifer Caffarella, Ben Isett
68 John Morgan

Hours: 9 am – 5 pm, Monday-Friday


The Penn Microarray Facility provides instrumentation and expertise for RNA transcript profiling. DNA microarrays provide a highly parallel means of measuring the abundance of RNA for targeted genes in a biological sample. The Facility supports two microarray formats: oligonucleotide arrays synthesized by Affymetrix Inc. and arrays of probes 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. Researchers from the University of Pennsylvania and its affiliated institutions are invited to utilize the Microarray Facility as part of their functional genomics efforts, and projects from non-affiliated institutions will be considered by special arrangement. All projects are initiated only after consultation with the facility director; this will ideally occur during the experimental design stage to ensure maximal and meaningful results.

Lab work. Services include RNA isolation, clone set management, probe amplification and purification, microarray printing, target preparation including appropriate linear amplifications and labeling methods, array hybridization and scanning, and data formatting and analysis. Additional resources can be made available through the Facility for laser capture microdissection, cell sorting, library construction and clone set procurement.

Bioinformatics. Data analysis software associated with the Facility's instrumentation is available for client use both on and off-site. Tools for additional statistical analyses, database management, pattern recognition, and inter-project collaboration are available via the Facility's close ties to the Penn Genomics Institute. Bioinformatics consultations and training are available at www.genomics.upenn.edu.

Consultation. Appointments are available free of charge to discuss project-specific issues such as experimental design, resource identification, project status and data analysis. Please call Don Baldwin for more information, to schedule an appointment, or to arrange for a seminar or group discussion about transcript profiling and functional genomics.


GeneChip oligonucleotide microarrays. An Affymetrix package containing two four-place fluidics stations, GCS3000 laser scanner, GeneChip hybridization oven and computer workstation is used for processing GeneChip oligonucleotide arrays. These microarrays are available for gene sets from human, rat, mouse, Arabidopsis, Drosophila, yeast, E. coli and other organisms, and are available to Facility clients at substantial discounts under Affymetrix contract pricing with the University of Pennsylvania, the Cancer Center, Children's Hospital of Philadelphia and the Wistar Institute. Under the current Affymetrix Core Lab Program, Penn Microarray Facility clients can request personal copies of the software necessary to visualize GeneChips and re-quantitate results using a variety of analysis options.

Glass slide cDNA microarrays. A GeneMachines OmniGrid microarraying robot deposits oligomers or PCR amplified probes onto treated microscope slides using 48 pins, producing an array of up to 20,000 probes per slide. Automated slide hybridization and washing can be performed on the Tecan hyb station. Hybridized arrays are scanned with an Axon GenePix scanner. Commercial and custom clone sets are processed and archived in 96- and 384-place microplates using a Beckman BioMek FX robotic workstation, two MJ Research Tetrad thermocyclers and various smaller instruments for microplate spectrophotometry, centrifugation, nucleic acid purification and electrophoresis.

Last Updated on 7-15-04

Facility Description
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Forms and Guidelines
Array Examples
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