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
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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 InfoFor additional information or to set up an initial consultation, please contact: Jonathan Schug, Ph.D. |
Shipping InfoWhen 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 |
Special Pricing for DRC/IDOM MembersThrough the support of the NIDDK Research Center grants we are able to offer the Institute for Diabetes, Obesity, and Metabolism (IDOM; P30DK19525), Diabetes Research Center (DRC, 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 Functional Genomics Core in any ensuing research publications. FGC Analysis CalendarUse this calendar to track progress of more complicated, long-term, analyses at the FGC. You can open the link in a browser or subscribe to the calendar using the ICS file. Activities are coded by an experiment number which we give you shortly after the initial consultation. HTML: https://zimbra.upenn.edu/home/jschug@zimbra.upenn.edu/FGC-Public.html ICS: https://zimbra.upenn.edu/home/jschug@zimbra.upenn.edu/FGC-Public.ics TessLA Website LinkWe load high-throughput sequencing data into the TessLA genome browser to visualize the results, to act as a hub for further analysis, and to integrate data across multiple experiments from your lab. Data is password protected. We will send you a password as the data becomes available.
GLITR: A Chip-Seq Analysis ProgramGLITR was developed by Geetu Tuteja in the Kaestner Lab as a way to call regions of enrichment in ChIP-seq data. We have used it successfully for TF-ChIP as well as histone modification ChIP and it is a standard part of our analysis pipelines. It is available for download at GLITR website. |
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