Diabetes Genome Anatomy Project

Core Labs > Joslin Genomics Core

Joslin Genomics Core

Core Director: Mary-Elizabeth Patti, M.D. (Joslin Diabetes Center)
Staff: Martha Vokes
Contact: martha.vokes@joslin.harvard.edu

Specific Aims

The Joslin Genomics Core Facility provides microarray expression profiling related to both rodent and human projects, currently utilizing high-density oligonucleotide arrays (Affymetrix). In the context of the DGAP, the Genomics Core will analyze expression profiles of RNA samples produced from rodent and animal models of normal and abnormal physiology in DGAP experiments.

The core facility is presently staffed by Dr. Mary Elizabeth Patti, Core Director, and Martha Vokes, technical director. Since opening in November 2000, the Core has been providing sample preparation, hybridization, and analysis services, with over 1200 arrays processed to date. A dedicated DGAP core technician will perform all cDNA/IVT reactions for DGAP samples in order to minimize preparation-related variability. Moreover, we will utilize an optimized protocol for RNA extraction and cRNA synthesis which will also be utilized by the U-Mass Core. The Core is responsible for maintenance of quality controls, reagents, provision of primers, and test arrays. All hybridization data are immediately published to the LIMS database and are securely accessible to each investigator via the Joslin and DGAP networks.

Quality Control Measures

The core facility maintains a continuously updated record of array background and hybridization efficiency (percent genes detected for a given array) to permit analysis of trends which might influence data outcomes. For each sample, prokaryotic hybridization controls (Bio B, C, D, and Cre) are spiked into the sample and hybridization cocktail to permit analysis of hybridization sensitivity. We are consistently detecting transcripts at the <1.5 pM level (lowest concentration of spiked control). Future plans call for the genomics core lab to provide species-specific RNA standards to permit standardization of data analysis across multiple laboratories.

Related Projects

• Project 2: Identifying the underlying alterations in gene expression which result in type 2 diabetes