Available equipment

Rhode Island NSF EPSCoR research facilities and services are open to users from each of our partner institutions around the state. Being part of the EPSCoR network also gives scientists access to other equipment at our partner institutions. Please contact the person listed for each institution for details on specific equipment and services.

URI MSRFMarine Science Research Facility (University of Rhode Island, Narragansett)

Ed Baker

  • Services include equipment training, consultation on experimental design and set up, and aquarium tours.
  • Coming soon – Beckman Coulter Counter for live and fixed samples and Visualization lab including microscopes, high definition cameras and computers with large screen monitors
  • -20 Freezer
  • Autoclaves (1 large, 1 small)
  • Balance
  • BD Influx flow cytometer and technician
  • Cell counting chambers
  • Clean Bench
  • Environmental chambers
 (4 100 sq.ft. each, 2 range from 4-24C, 2 range from -4-24C)
  • Eppendorf microcentrifuge
  • Eppendorf PCR machines (2)
  • Filter manifold with 25 and 47 mm filter cups
  • FIRe Flourometer (Fluorescence Induction Relaxation Fluorometer)
  • Flow cam
  • Gel visualization box
  • Handheld YSI
  • Heating/cooling block
  • Homogenizer
  • Incubated shaker
  • Laboratory fridge/freezer
  • Lachat Nutrient Auto-Analyzer
  • Laminar Flow Tank
  • Light Meter
  • Membrane Inlet Mass Spectrometer (MIMs)
  • Micropipettes (12)
  • Milli-Q water system
  • Nanodrop
  • Nikon Inverted Scope with Hoffman Contrast
  • Olympus Stereomicroscope
  • Percival incubator with dimmable lights
  • pH meter
  • Pipettes
  • Polytron homogenizer and generator
  • Respirometer Tank
  • Shakers (5)
  • Small Strip tube centrifuge
  • Sonifier
  • Spectra Max Plate Reader
  • Stingray Microscope Camera
  • Stratagene Q-PCR MXx3005P
  • Turner 10-AU fluorometer
  • Vacuum pump
  • Vortex
  • Walk in -20 degrees C freezer
 (185 sq.ft.)
  • Water bath
  • Wet lab space with large flow capacity of filtered, ambient/chilled/heated seawater, raw seawater, UV treated seawater, air supply, alarm and monitoring systems, dedicated ozone treatment for transgenic and pathology lab effluent (3 buildings, 7,200 sq.ft. and nearly unlimited exterior space including mesocosm tanks)

RIGSC EPSCoRGenomics and Sequencing Center (CBLS, University of Rhode Island, Kingston)

David Nelson
Paul Johnson

Services include DNA sequencing and fragment analysis (Sanger method), next generation sequencing and library preparation (Illumina MiSeq), light and scanning confocal microscopy, and genomics equipment use (qPCR, BioAnalyzer, Nanodrop, etc.).

  • AirClean 600 PCR Workstation – combines an ISO 5 / Class 100 clean air environment with UV light sterilization to provide optimal protection from sample contamination.
  • Agilent 2100 BioAnalyzer
 – microfluidics-based platform for sizing, quantification and quality control of DNA, RNA, proteins and cells.
  • Applied Biosystems 3130xl and 3500xl genetic analyzers
 – fluorescence-based analysis systems used for DNA sequencing and fragment analysis.
  • Beckman Coulter Allegra 25R – refrigerated centrifuge.
  • CLCbio Genomics Workbench – software for assembling, comparing, and visualizing next generation sequence data from the MiSeq.
  • Covaris S220 AFA ultrasonicator – used to shear or fragment DNA samples for the preparation of sample libraries for analysis in next generation sequencers.
  • DNAStar Lasergene server
 – comprehensive suite of software for DNA & protein sequence analysis, contig assembly and sequencing project management
  • Eppendorf epMotion 5075 VAC  – automated liquid handling workstation for diverse methods such as nucleic acid purification, PCR setup, cleanup of sequencing reactions, etc.
  • Eppendorf Mastercycler ep Gradient S thermal cycler
s (2).
  • Illumina MiSeq next generation sequencer – used for a wide range of genetic analyses including whole-genome sequencing, mRNA sequencing, de novo sequencing, ChIP-Seq, targeted resequencing, and metagenomics (16S rRNA sequencing).
  • IntegenX Apollo 324 – automated workstation for next generation sequence library preparation using bead technology to execute high-performance isolation and purification of nucleic acids (DNA, RNA, plasmids, etc.) and proteins.
  • Invitrogen Qubit fluorometer – provides highly accurate quantification of DNA, RNA and protein samples.
  • MJ Research PTC-100 thermal cycler
  • Nanodrop 8000 (8-channel spectrophotometer)
 – measures concentration and purity of DNA, RNA and protein samples.
  • OmniLog Phenotype Microarray System
 – used to identify bacterial species and determine their phenotypic behavior on a wide variety of substrates and compounds.
  • Qiagen TissueLyser
 – provides rapid and efficient disruption of cells and tissues.
  • Qiagen QiaCube – automated workstation to process Qiagen spin columns for purification of plasmid DNA, genomic DNA, RNA, viral nucleic acids, and proteins
  • Roche LC480 qPCR instruments (2)
 – plate based real-time PCR platform for highly accurate qualitative and quantitative detection of nucleic acids and genotyping.
  • Stratagene (Agilent) Mx3005 qPCR system
 – used to quantify nucleic acids for studying gene expression, mutational analysis, disease state, and gene dosage.
  • Sage Science BluePippin – a preparative electrophoresis platform that separates, sizes and extracts DNA fragments.
  • Thermo Savant DNA SpeedVac
 – a centrifugal concentration system for drying low-volume ethanol or isopropanol precipitates of DNA and RNA.
  • Vibratome 5000 cryostat – uses a microtome housed inside a chamber with a temperature of -35°C for the preparation of frozen sections of cells and tissues.
  • Zeiss AxioImager 2 motorized microscope with AxioCam high-resolution digital camera and
 LSM 700 scanning confocal module with 4 lasers at 405, 488, 555, & 639 nm excitation

NSF:EPSCoR Shared Proteomics FacilityNSF/EPSCoR Shared Proteomics Facility (Brown University, 70 Ship Street)

Mandar Naik, Ph.D.

  • Agilent 1200 High Performance Liquid Chromatography (HPLC)
  • AKTAprime Plus Liquid Chromatography (LC)
  • FluoroMax-4 Spectrofluorometer
  • Fourier transform ion cyclotron resonance mass spectrometry
  • Jasco J-815 Circular Dichroism (CD) Spectropolarimeter
  • Microcal VPViewer-Differential Scanning Calorimeter
  • Microcal VPViewer-Isothermal Titration Calorimeter
  • NanoDrop8000
  • Thermo Linear Trap Quadropole (LTQ) Orbitrap Velos mass spectrometer

Other Resources for EPSCoR Scientists and Students

Center for Computation and Visualization (Brown University) 

  • Highest priority access to the EPSCoR 512-core condo maintained and supported by the CCV
  • Access to a Galaxy portal with 128 cores and 512 GB memory per node (2 nodes)
  • Data Storage purchase (CCV priced at $750 per TB) and includes automatic backup and storage for up to six years
  • Highest priority access to the Scale-MP “Fat Node” of 1.5 TB which is extremely useful for de novo genome assembly from fragment reads
  • Access to over 100 bioinformatics/genomics applications and general applications

Bioinformatics Support

  • Collection and assembly of data for genomic analysis and for gene expression profiling
  • General source of advice on existing tools for genome analysis, gene expression analysis, gene annotation, and epigenetic analysis
  • Analysis of basic biological research and biomedical data using existing tools
  • Evaluation and development of new and advanced bioinformatics tools and analytical software
  • Development and description of data workflows and pipelines
  • Flexibility to work with data streams from various major instrumentation platforms
  • Technical and analytical methods  preparation for assembly of grant applications

Software tools

  • MicroArray software:  Bioconductor
  • Pathway analysis:  IPA
  • RNA-Seq software: CASAVA, Tophat/Cufflinks, CrossBow, Erange, GATK
  • CHIP-Seq software: PeakSeq, SPP package, MACS
  • De Novo Assembler: ABYSS, SOAPDenovo, Velvet, InchWorm, Rnnonator,  Agalma
  • Aligner: Eland, Bowtie, MAQ, Blast, BWA
  • CNV analysis: CNVnator
  • MicroRNA analysis: miRExpress
  • Other tools: samtools, igvtools, bfast, bamtools, Bioperl, BioPython

Nature Lab (Rhode Island School of Design) 

Institute for Computational and Experimental Research in Mathematics (ICERM)

Other Resources at each partner institution

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