RI-INBRE Centralized Research Core Facility (CRCF)  https://web.uri.edu/riinbre/core-facility/  is funded by RI-IDeA Network of Biomedical Excellence (INBRE, P20GM103430, PI: Bongsup Cho) and is managed by Dr. Ang Cai with assistance from Research Associate III Janet Atoyan. The CRCF is a state-wide core facility to promote interdisciplinary and cutting-edge biomedical research and student training opportunities by providing researchers access to advanced chemical and molecular biological instruments.

The CRCF houses over 40 high-end molecular-biology, analytical, and imaging instruments to serve RI’s biomedical scientists totaling 3800 sq. ft. in the URI College of Pharmacy building. Inside the main laboratory space, a cell culture suite contains a biosafety cabinet and two incubators. A separate NMR and Mass Spectrometry laboratory includes a NMR spectrometer and two mass spectrometers.

The staff trains and assists users to operate any CRCF instrumentation that may be needed in their research. As a training-focused cost center, the CRCF does not provide project-based analytical and technical services. 

Major equipment includes:

• Sciex LC/MS Triple TOF 4600 Mass Spectrometer – Accurate mass triple quadrupole MS and MS/MS for for qualitative and quantitative workflows with a mass range to 40,000D. LC is a Shimadzu Prominence liquid chromatograph with additional UV detector.
• Shimadzu Axima Performance MALDI-TOF MS – Matrix assisted laser desorption and ionization MS for peptides, proteins and DNA with a mass range to 500,000D.
• Agilent LC/MS 6470B Triple quadrupole Mass Spectrometer – Nominal mass triple quadrupole MS for quantitative workflows with a mass range m/z 5-3000.
• Nikon Eclipse Ti2 Inverted Confocal Microscope – Imaging for transmitted light, epifluorescence light, and laser confocal techniques. Confocal laser frequencies at 405, 488, 561 and 640 nm. Motorized XYZ stage.
• Cytiva BiaCore T200 SPR – a microfluidic platform for measuring binding between biomolecules using surface plasmon resonance optical technology.
• BD FACSVerse Flow Cytometer – counts cell populations based on fluorescent labels.
• Agilent Seahorse Metabolism Analyzer – measures changes in cellular energetics in real-time using a 96-well format.
• BioTek Cytation 5 Imager – Multimode plate reader and imager with temperature- and atmosphere-controlled sample chamber.
• Bioautomation MerMade 4 DNA Synthesizer – For preparation of DNA sequences using chemically-modified or standard nucleotides.
• Roche LightCycler 96 qPCR – Quantitative PCR instrument for measuring DNA amplification and gene expression by detecting fluorescence in real-time.
• Azure Biosystems Sapphire Imager – Multi-mode laser imager, capable of RGB, fluorescence and phosphor imaging. Lasers at 488nm, 520nm, 658nm, and 784nm.
• Li-Core Odyssey CLX IR Imager – Western blot and gel imager using IR fluorescence dyes at 700 and 800nm.
• Nanotemper Tycho NT.6 Protein Quality Analyzer – Verifies protein quality by measuring unfolding in a three-minute assay.
• Beckman Optima L-100XP Ultracentrifuge – Capable of 100,000 rpm with multiple acceleration and deceleration profiles. Type 70 Ti, Type 70.1 Ti, Type 90 Ti and SW 40 Ti swinging bucket rotors available.

The RI-INBRE Molecular Informatics Core (MIC)  https://web.uri.edu/riinbre/mic/ was formed from the merger of the RI-INBRE Bioinformatics Core and the sequencing component of the RI Genomics and Sequencing Center, a URI NSF EPSCoR facility. The MIC is an NIH Data Sciences Core for Biomedical Research facility and provides sequencing and bioinformatics support for URI and other institutions in the INBRE and EPSCoR networks.

The MIC is under the direction of Dr. Chris Hemme (Biomedical and Pharmaceutical Sciences, College of Pharmacy) and sequencing manager Janet Atoyan. The Core offers services in four general areas: 1) Sequencing and Sample Prep, 2) Bioinformatics and Data Science, 3) Molecular Modeling, and 4) Virtual Reality. The Core is working to establish start-to-finish pipelines that allow users to access any services from sample prep to sequencing to bioinformatics analysis and works with the RI-INBRE CRCF to provide a unified pipeline between select data generation and data analysis projects. We also provide access to molecular modeling software such as Spartan and Molecular Operating Environment. The Core maintains the College of Pharmacy virtual reality hardware and works with URI ITS and other collaborators to develop STEM-based VR apps for use in teaching, training and research.

The Biomedical Data Science component of the Core focuses on omics data analysis, biostatistics, general data science, and training. The Core primarily utilizes the URI high performance computing resources but is working with URI Research Computing and the NIH STRIDES initiative to increase access to cloud resources.

Bioinformatics Resources and Virtual/Augmented Reality Equipment

• 2 bioinformatics desktops/3 VR laptops – two desktops located at URI loaded with a variety of software for molecular modeling, bioinformatics and virtual reality applications
• HTC Vive/3 HTC Cosmos VR Headsets – Virtual reality headsets available for use for teaching and training
• Spartan License – Software for molecular modeling with an emphasis on small molecules
• Molecular Operating Environment (MOE) License – Software for molecular modeling with an emphasis on large molecules (eg proteins)

The Sequencing Component of the Core currently offers both analytical and equipment services using the following instrumentation:

• ABI 3500xl genetic analyzer – DNA Sanger sequencing and fragment analysis
• Takara Bio Apollo 324 library prep system – NGS gDNA library preparation
• Illumina MiSeq – next-generation sequencing

Additional Sequencing Resources include