FACILITIES AND OTHER RESOURCES
University of Connecticut – Center for Genome Innovation
The Center for Genome Innovation (CGI) is housed within the Institute for Systems Genomics on the University of Connecticut. The CGI, an open-plan laboratory, occupies 2000 ft2 in the recently constructed, state of the art Engineering and Science Building on the Storrs Campus. The CGI has a staff of 6 sequencing/administrative staff and has established high throughput library preparation and sequencing capacity including all necessary ancillary equipment for the following sequencing platforms: Illumina NovaSeqX+, MiSeq (x2), Illumina NextSeq 550 (x1), Illumina NextSeq 2000 (x1), Illumina i100+ (x1), Oxford Nanopore MinION (x5), GridION (x1) and PromethION-24 (x1), PacBio Sequel IIe and a PacBio Revio (x1). The Illumina NextSeq 550 sequencer on the Storrs campus is used to scan Infinium CytoSNP 850K and Infinium EPIC Methylation arrays for human samples only.
The CGI offers both supervised and unsupervised access to most instrumentation and training for use and implementation, along with an option to process samples through a fee-for-service structure. The CGI is also capable of assisting with protocol development for various applications and technologies.
The lab is equipped with both standard and high throughput molecular biological equipment. Sample preparation robots include: SPT LabTech Firefly +, Kingfisher Apex, Eppendorf epMotion 5075 TMX and Opentron OT-2 liquid handling robots (single and 8 channel pipetting from 0.1ul 1000ul), Qiagen QiCube and QiAgility. Thermal cyclers for standard and quantitative PCR (CFX384 Real Time x2, CFX96 Real Time x2, and 96 and 384 well thermocyclers), standard and automated gel electrophoresis systems, centrifuges, single and multichannel micropipettors, water baths, incubators, refrigerators and freezers for sample and reagent storage. Specific (major) equipment available for use include the: Beckman Allegra X-12R Refrigerated Centrifuge, Eppendorf 5910R Centrifuge, Agilent TapeStation 4200 (x2), Agilent Femto Pulse, Qiagen QiAxcel electrophoresis system, Qubit 3.0 (x2), PCR hoods (x2), chemical and biosafety hoods, Pippin Prep (including Pippin Prep, Blue Pippin and Pippin HT systems), Covaris M220, S2 and Cryoprep, S2 Genomics Singulator. Lastly, the CGI has a BioRad QX200 Droplet Digital PCR instrument which can be used for absolute copy number, mutation and gene expression detection.
On-site training and outreach at UConn can be performed in the training facility in the Institute of Systems Genomics space. This space, within the Center for Genome Innovation, includes a training laboratory for molecular work, two working classrooms equipped for distance and in person learning, a computational training space, all located on the same floor (3rd). In addition, we have a large, multi-format lobby and auditorium space with moveable tables, projection and both large and small format interactive space that seats 80 people. Moreover, a historical display of the evolution of sequencing technologies is in the CGI lobby, offering an outreach launch point for discussion of genomic technologies and advances.
University of Connecticut – Computational Biology Core
The Computational Biology Core (CBC)is housed within the Institute for Systems Genomics at the University of Connecticut. The CBC has a staff of three full time bioinformaticians that provide training and consultation services to the research community at all of the UConn campuses. High Performance Computing (HPC) resources, including the Xanadu and Mantis clusters, are housed in a secure data center at the Cell and Genome Sciences Building on the UCHC Farmington campus. All servers are freely available to members of the UConn research and their research affiliates. The compute clusters are comprised of 75 compute nodes with over 10,000 CPU cores, 105 TB of RAM, and capable of processing at 300 TFLOPs. The nodes are a mix of Dell C6145 chassis with four 12-core AMD Opteron processors and Dell R730 chassis with two, 18-core Intel Xeon E5-2697v4 processors. Node memory ranges from 256 GB to 2 TB of RAM. Additional resources include 2688 NVIDIA M2075 GPU cores. All nodes are equipped with ten-gigabit interfaces and connected to a 10/40/100 gigabit network infrastructure. Isilon and Qumulo Network Attached Storage systems are provided with a capacity of 15 petabytes. An additional 3.8 petabytes of geo-spread object storage is provided via an Avere gateway with 30 gigabit-per-second aggregate throughput.
All clusters allow access to over 400 bioinformatic modularized and/or containerized applications. These applications support analysis in phylogenetics, metagenomics, genome assembly, transcriptome assembly, sequence alignment, sequence annotation, variant detection, Chip-Seq, proteomics, and a variety of visualization tools.