Computational Genomics Core

Example of data analysis field using ImaGene software

The Computational Genomics Core provides neuroscientists and other Tufts investigators with resources for gene expression and genomics studies, pathways analysis and computational biology. Bioinformatics software applications, such as GeneSpring and Bioconductor for microarray analysis, are available on CNR workstations located in Stearns 328. Core users can reserve a computer by contacting Mr. Chris Parkin and signing up in the facility logbook. A web interface for the Tufts Bioconductor suite (CARMAWeb) is now available. A tutorial for CARMAWeb can be found at this link. You can learn more about the Tufts Bioinformatics Server at this link. Contact Dr. Lax Iyer or Mr. Chris Parkin with questions about core services.

Services of the Genomics Core

• Nucleic acid quality analysis
• RNA/DNA labeling
• Affymetrix gene expression (microarray) studies
• Initial analysis of microarray data using ImaGene software
• Statistical analysis of microarray data using GeneSpring, Bioconductor and other software packages
• Training sessions on Genomics Core programs
• Access to Accelrys GCG package for sequence analysis
• Licensing and installation of program software
• Genomics and Bioinformatics consultations

The CNR Genomics Core includes the Tufts Expression Array Core (TEAC) which provides instruments and expertise for gene expression studies (located on Stearns 2). There are instruments for nucleic acid analysis (Nanodrop and Agilent Bioanalyzer), 2 Q-PCR machines (Stratagene real-time cyclers), and Affymetrix microarray analysis (GeneChip system 3000). To reserve the Affymetrix instrument, or Bioanalyzer, please contact Mr. Chris Parkin and sign up in the appropriate facility logbook. To use the Stratagene real-time cyclers, sign up on the calendar at Q-PCR Mx4000 and Q-PCR Mx3000P.

The current Tufts-negotiated prices for Affymetrix gene chips can be found at this link. Please contact Mr. Parkin for current pricing of microarray services and use of facility instruments (Bioanalyzer and Q-PCRs).

In addition to gene profiling services, the CNR Genomics Core subsidizes access to mass spec services for neuroscientists (in the Tufts Molecular Core). These and other CNR core services are subsidized for neuroscientists through the new CNR Core Award.

Links of Interest
• Fees for CNR Bioinformatics Services
• FAQ regarding Affymetrix Gene Expression Studies
• Websites endorsed by the Genomics Core of the Center for Neuroscience Research
• Tufts Seqweb Server (for Tufts use only - requires an account)
• University of Pittsburgh Online Bioinformatics Resources Collection
• Bioinformatics Links Directory
• Neuroscience Informatics Resources

Images produced using GeneSpring software for data analysis of mouse genes. Left: k-Means clustering; Right: graph of gene expression allows for visualization of results. * Core directors receive discounted rates for core services to offset time and    effort spent with core and center administrative duties.