The Genomics and Bioinformatics Core Facility provides many levels of support for the successful completion of projects in several ways, including genomics support, bioinformatics support, and access to computing resources. We also provide grant support to assist investigators in accelerating their research programs.
GENOMICS & BIOINFORMATICS CORE FACILITY STATEMENT
The facilities at University of Notre Dame will support the successful completion of this project in several ways. The Notre Dame Genomics and Bioinformatics Core Facility (GBCF) is a 1500 square foot facility that houses specialized equipment for DNA and RNA sequencing and microarray applications including Illumina MiSeq and NextSeq 500 sequencers, Applied Biosystems 3730xl 96-capillary sequencer, Agilent 2100 Bioanalyzer, Affymetrix GeneChip System (including the GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450, and GeneChip Scanner 3000 7G), Roche NimbleGen 4 and 12‐bay hybridization systems, Roche NimbleGen MS 200 scanner, Qubit 2.0 Fluorometer, BioRad CFX384 Real-Time PCR Detection System, Nanodrop 2000 Spectrophotometer, Sage Science BluePippin, Invitrogen E-Gel iBase Power System, and Covaris S220 high-intensity acoustic shearing equipment. Cost effective sequencing for large-scale sequencing projects is achieved by outsourcing through negotiated contracts. A Managing Director and 2 research technicians are employed full-time in the genomics lab and are responsible for operating and maintaining the equipment listed above and have received training from respective manufacturers in machine maintenance and experimental methods.
The GBCF also provides bioinformatics support for the analysis of genomic data. The bioinformatics team is lead by Dr. Scott Emrich, Bioinformatics Director and Associate Research Faculty, with a primary academic appointment in the Department of Computer Science and Engineering. Dr. Emrich has expertise in sequence assembly, next-generation sequence analysis, and parallel computing. His role includes high-level oversight of bioinformatics staff, facilities and equipment, and strategic planning for maintaining state-of-the-art bioinformatics capacity. The GBCF has developed pipelines for downstream data analysis of next-generation short-read sequencing data. Particularly relevant to most projects is the availability of well-developed pipelines to assemble short read sequences, extract SNPs, and analyze population genomic data. Dr. Emrich’s team, including a full-time Senior Analyst, provides analysis and consulting to assist GBCF users with all phases of a project from experimental design to data management and downstream analysis.
There are two primary classes of computing resources that the GBCF uses: 1) high memory machines (up to 1 TB, tens of cores) prioritized for bioinformatics research, and 2) the university’s Center for Research Computing (CRC), a large shared computational resource with accompanying research data backup and archival storage.
The CRC operates a state of the art High Performance Computing (HPC) facility providing advanced computing support to researchers within Notre Dame, the local community and industry. The facility is highly secure and reliable and can be accessed securely and seamlessly. The High Performance Computing (HPC) team manages parallel supercomputers, clusters, grid networks and storage (around 23,000 cores and 3000TB of storage) which provide exceptional levels of processing speed and power. The GBCF, aided by the CRC, is the perfect partner for any -omics focused project due to our expertise and these University wide resources.