Functional Genomics Core

Functional Genomics Core - Home

The global aim of the Functional Genomics Core is to provide our clients with a complete microarray and/or high-throughput sequencing package, from the initial steps of experimental design to the final steps of result interpretation and publication. The services we provide can be broken down into four main areas:

Sample Preparation and Quality

All samples submitted to the core must be analyzed for integrity using an Agilent Bioanalyzer. The Core has developed certain criteria for RNA and DNA samples that allow for optimum results for all our services. We have also troubleshooted many RNA/DNA isolation and amplification methods to help yield better results. We offer a full range of services including assessment of sample quality, linear RNA amplification, cDNA amplification, QRT-PCR, islet purity matching, batch slide scanning, image quantification, data and pathway analysis.

Agilent Microarray Studies

We provide consultation and advice on microarray experimental design and analysis. Our aim is to work with all investigators prior to their providing samples, so they can be trained in microarray experimental design, from the use of appropriate RNA isolation techniques to giving advice on data interpretation and publication of their experiment. The Core has developed highly sensitive methods for sample labeling, detection and microarray analysis. We can produce excellent data sets with as little as 5-25 ng total RNA, or the amount obtained from a single pancreatic islet.

High-Throughput Sequencing

We have a Illumina Genome Analyzer II which is currently capable of generating 10 million aligned reads per lane of up to 50bp each. We have experience with ChIP-seq, nucleosome mapping, miRNA, and genome resequencing in mouse, human, zebrafish, and others. We offer advice to achieve successful library prepartion. You can get the raw results, BED files for uploading to the UCSC genome browser, or have us do much of the initial analysis for you. We have our own genome browser for rapid visualization of results.

Advanced Data Analysis

We have developed significant technical expertise in the area of microarray analysis, and can provide data analysis and bioinformatics support as needed. We have expertise and are very interested in bringing together multiple data sets from different experiments to understand your biological system. Typical examples are looking for connections between multiple TF-binding or histone marks combined with gene expression and/or binding site enrichment to understand gene regulation in your system.

Contact Info

For additional information or to set up an initial consultation, please contact:

Jonathan Schug, Ph.D.
Department of Genetics, IDOM
752A Clinical Research Building
415 Curie Boulevard
Philadelphia, PA 19104-6145
Tel: +1 (215) 898-0773
Fax: +1 (215) 573-2326
E-mail: jschug@mail.med.upenn.edu

Shipping Info

When shipping samples to us, be sure to use plenty of dry ice, ship overnight, but do not send on Friday. The shipping address is:

Alan Fox or Olga Smirnova
Department of Genetics, IDOM
750 Clinical Research Building
415 Curie Boulevard
Philadelphia, PA 19104-6145
Tel: +1 (215) 898-0772

Special Pricing for IDOM Members

Through the support of the NIDDK Research Center grants we are able to offer both Institute for Diabetes, Obesity, and Metabolism (IDOM; P30DK19525) and Center for Molecular Studies in Digestive and Liver Diseases (CMSDLD; P30DK50306) members substantial discounts on the cost of these services. Please remember to acknowledge these centers and the services of the Genomics and Gene Targeting Core in any ensuing research publications.