Center for Biomedical Data Science | Facilities and Resources

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Center for Biomedical Data Science

Using big data to detect and treat diseases earlier, faster, and better. 

 

 

Facilities and Resources

Find facilities and resources spanning molecular biology and computing facilities, across the state of Oregon. 

The University of Oregon's core facilities are supported by the Office of the Vice President for Research and Innovation and are available to researchers from UO, other academic institutions, and industry partners. Each facility provides training opportunities and expert consultation in addition to access to state-of-the-art instrumentation. 

Genomics and Molecular Biology 

 

Genomics and Cell Characterization Core Facility (GC3F)

  • Comprehensive genomics, flow cytometry, and imaging services
  • Services include: Sanger DNA sequencing, microarray genotyping/printing, Illumina high-throughput sequencing (HiSeq 4000, MiSeq, NextSeq 500), PacBio long-read sequencing (Sequel system), flow cytometry, and advanced microscopy 

University of Oregon (UO)

Integrated Genomics Laboratory

  • Comprehensive RNA and DNA analysis
  • Services include: consultation, nucleic acid extraction, bulk and single cell sequencing, targeted gene analyses, and data processing, DNA services, gene profiling, massive parallel sequencing and QC. 

Oregon Health & Sciences University (OHSU)

Epigenetics Consortium

  • Sample preparation and bioinformatics for DNA methylation, chromatin conformation, and gene expression.
  • Services include: end-to-end support for a number of DNA methylation and chromatin analyses, including  Bisulfite DNA sequencing and HiC. 

Oregon Health & Sciences University (OHSU)

Proteomics

  • Mass spectrometry for protein identification, post-translational modifications, and relative abundance profiling.
  • Services include: protein identification, partial sequencing, identification and localization of post-translational modifications, quantitative comparison of protein abundances in complex mixtures using 11-plex TMT labeling, identification of protein/protein interactions by analysis of affinity purified complexes, targeted MRM analysis on known proteins, determination of whole protein mass and preparation of submissions for public data repositories 

Oregon Health & Sciences University (OHSU)

 

Imaging and Microscopy 

 

Genomics and Cell Characterization Core Facility (GC3F) Light Microscopy

  • Multiple confocal and super-resolution microscopes
  • Equipment includes: Olympus Fluoview FV1000, Leica SPE, GE DeltaVision Ultra, Zeiss LSM 880 with SIM and Airy Scan, Nikon CSU-W1 SoRa Spinning Disk with TIRF, custom light-sheet microscope 

University of Oregon (UO)

X-ray Imaging Core Facility

  • Non-destructive X-ray based 2D and 3D imaging
  • Equipment includes: Zeiss Xradia 620 Versa (microCT/X-ray microscopy), Scanco vivaCT80 (in vivo microCT), Faxitron Ultrafocus (in vivo radiographs) 

University of Oregon (UO)

Advanced Imaging Research Center

  • Specializes in MRI and MRS techniques with 3T, 7T, and 11.7T MRI instruments.
  • Equipment includes: Siemens 3T, Siemens 3T (ONPRC), Siemens 7T, Bruker 11.75T. 

Oregon Health & Sciences University (OHSU)

Advanced Light Microscopy Core

  • Advanced fluorescence microscopy for cells, tissues, and animals.
  • Equipment includes: Zeiss LSM 980 with Airyscan 2, Zeiss LSM 900 with Airyscan 2, Yokogawa CSU-W1 spinning disk confocal on a Nikon TiE, Andor BC43 benchtop spinning disk confocal, Zeiss Apotome.2 on an Axio Imager, Zeiss Celldiscoverer 7, Zeiss Elyra 7 with lattice SIM, Sartorius IncuCyte S3, and more.  

Oregon Health & Sciences University (OHSU)

Multiscale Microscopy Core

  • State-of-the-art electron and light microscopy services.
  • Equipment includes: Talos 120C Transmission Electron Microscope, FEI Helios G3 DualBeam™ Scanning Electron Microscope, FEI CorrSight, Thermo Fisher Helios UC5 DualBeam™ Scanning Electron Microscope, FEI Vitrobot, Pelco EasiGlow 91000 Glow Discharge Cleaning System, Leica ACE600 Coater, Leica Critical Point Dryer CPD300, UC7 Ultramicrotome, RMC-Boeckeler ASH-100 and more.  

Oregon Health & Sciences University (OHSU)

Small Animal Research Imaging Core

  • MicroPET-SPECT/CT, high-frequency ultrasound, and biophotonics imaging for in vivo studies.
  • Services include: biophotonics, ultrasound, and MicroPET-SPECT/CT. 

Oregon Health & Sciences University (OHSU)

 

Neuroimaging and Cognitive Science 

 

Lewis Center for Neuroimaging (LCNI)

  • MRI facility for cognitive neuroscience and biological imaging.
  • Equipment includes: Siemens Skyra 3T and Prisma 3T MRI systems, full MR coil design and fabrication capabilities. 

University of Oregon (UO)

 

Materials Characterization 

 

Center for Advanced Materials Characterization in Oregon (CAMCOR)

  • Full-service materials characterization center in Lorry I. Lokey Laboratories.
  • Services include: Electron microscopy (TEM, SEM-FIB), surface analysis (XPS, ToF-SIMS, Auger, AFM, FTIR, Raman), X-ray analysis, NMR, thermal analysis (TGA, DSC), rheometry. 

University of Oregon (UO)

Polymer Characterization Facility (CAMCOR)

  • Thermal and mechanical analysis of polymeric materials.
  • Equipment includes: DSC, DMA, TGA, TMA, rheometers, universal materials testing. 

University of Oregon (UO)

Elemental Analysis Core

  • ICP-MS for elemental content determination
  • Services include: methylmercury analysis, ICP-MS to determine the concentrations of chosen elements from various sample types and more.  

Oregon Health & Sciences University (OHSU)

 

Computing, Data Science, and Bioinformatics 

 

Research Advanced Computing Services (RACS)

  • High-performance computing and data services
  • Features include: Talapas supercomputer (250+ trillion calculations/second), storage, high-speed data transfer, consulting services

University of Oregon (UO)

Advanced Computing Center

  • Provides consulting, research storage, application hosting, and support for research computing systems.
  • Services include: consulting, HPC cluster access, tiered research storage solutions, secure local and remote collaboration options, virtual server environments, application hosting and license management/compliance, co-location and support for research computing systems, secure and public web portals, a large suite of open source applications running on a parallel computing cluster and provisioning for private compute clusters that are scaled and configured to meet the needs of individual customers. 

Oregon Health & Sciences University (OHSU)

Bioinformatics

  • Experimental design and analysis for high-dimensional data (RNA-seq, DNA-seq, ChIP-seq, CyTOF), plus data stewardship and management
  • Services include: Helping researchers leverage EHR/Epic data for studies, developing software and customized databases for clinical research data collection and management and assisting researchers with the storage, retrieval, sharing, and optimal use of biomedical information, data, and knowledge.   

Oregon Health & Sciences University (OHSU)

Bioinformatics & Biostatistics Core (BBC) at ONPRC

  • Supports biostatistics and DNA/RNA-sequencing bioinformatics, study design, and grant support
  • Services include: data analysis and manuscript preparation services falling in two main categories: 1) Biostatistics, such as statistical genetics, longitudinal, survival, and high-throughput/high-dimensional omics data analysis; and 2) Bioinformatics, such as DNA- and RNA-seq alignment, single-cell DNA- and RNA-seq analysis, variant calling, differential expression and pathway analysis, data integration, online data submission, and custom script writing. 

Oregon Health & Sciences University (OHSU)

Biostatistics & Design Program

  • Statistical guidance, analysis, and study design for proposals, grants, and research projects.
  • Services include: Proposal development, study design, statistical analysis planning, sample size and power analysis, statistical analysis planning, review of study instruments or survey implementation, sampling and randomization schemes. 

Oregon Health & Sciences University (OHSU)

Knight Biostatistics Shared Resource

  • Comprehensive biostatistics support specifically for cancer research at the Knight Cancer Institute. 

Oregon Health & Sciences University (OHSU)

Flow Cytometry and Cell Analysis 

 

GC3F Flow Cytometry Core

  • Cell sorting and analysis
  • Equipment includes: Sony SH800 cell sorter, Applied Biosystems Attune Cytometer (first generation) 

University of Oregon (UO)

Flow Cytometry and Monoclonal Antibodies

  • Cell sorting, analytical flow cytometry, and development of novel monoclonal antibodies 

Oregon Health & Sciences University (OHSU)

Histopathology

  • Specimen embedding, sectioning, staining, and immunohistochemistry.
  • Services include: Embedding Samples in either paraffin or optimal cutting temperature compound (OCT), sectioning using either microtome and cryostat to specified thickness, histochemical staining, testing and titering new antibodies, both monoclonal and polyclonal, avidin/biotin blocking steps and more. 

Oregon Health & Sciences University (OHSU)

 

Nanofabrication and Prototyping 

 

Knight Campus Clean Room

  • Class 1000 cleanroom for micro/nano-scale device fabrication
  • Capabilities include: Semiconductor and soft materials processing, integrated microsystems, bioengineering devices, nanoelectronics, nanophotonics, nanobiotechnology, environmental SEM with e-beam patterning 

University of Oregon (UO), Knight Campus

Oregon Fabrication and Design (OFAD)

  • Scientific instrument machine shop and 3D printing
  • Services include: Machining, fabrication, 3D printing (including 1-micron resolution polymer printing, composites, Two-Photon Polymerization), rapid prototyping 

University of Oregon (UO)

 

Chemical Analysis and Drug Development 

 

Bioanalytical/Pharmacokinetics

  • Small molecule analysis using LC-MS/MS, GC/MS, or HPLC 

Oregon Health & Sciences University (OHSU)

Biophysics Core

  • Access to state-of-the-art biophysics equipment

Oregon Health & Sciences University (OHSU)

Center for Radiochemistry Research

  • Radiosynthesis and quality assurance of radiolabeled molecules for imaging 

Oregon Health & Sciences University (OHSU)

Medicinal Chemistry Core

  • Medicinal chemistry expertise and organic synthesis support 

Oregon Health & Sciences University (OHSU)

Sterol Analysis Laboratory Core

  • Regulated bioanalytical services specializing in sterol analysis 

Oregon Health & Sciences University (OHSU)

 

Animal Research Facilities 

 

Aquatic Animal Care Services

  • Zebrafish and aquatic animal research support
  • Services include: Expert husbandry, research support for vertebrate genomics and development studies 

University of Oregon (UO)

Terrestrial Animal Care Services (TeACS)

  • Laboratory animal husbandry and veterinary care
  • Services include: Animal care, veterinary services, technical support for research using laboratory animals 

University of Oregon (UO)

Transgenic Mouse Models

  • Services include: cryopreservation, storage, and rederivation 

Oregon Health & Sciences University (OHSU)

Oregon National Primate Research Center (ONPRC)

Oregon Health & Sciences University (OHSU)

 

Biological Resources and Models 

 

BioLibrary

  • Fresh, frozen, OCT, FFPE tissues and blood derivatives, prospective blood collection 

Oregon Health & Sciences University (OHSU)

Fly Food Core

  • Provides Drosophila food to research labs 

Oregon Health & Sciences University (OHSU)

Virology Immunology Core

  • Production of viral vectors, virus stocks, antigens, and viral diagnostics 

Oregon Health & Sciences University (OHSU)

IMB Media Room

  • Glassware processing, media preparation and fly food preparation. 

University of Oregon (UO)

 

Plant Research 

 

UO Research Greenhouses

  • Over 6,000 sq ft greenhouse space plus one-acre field
  • Facilities include: Small greenhouse in Onyx Bridge Hall, central complex for research and teaching 

University of Oregon (UO)

 

Specialized Testing and Analysis 

 

Oregon Acoustic Research Laboratory (OARL)

  • Acoustics testing for mass timber assemblies, focus on supporting mass timber industry expansion 

University of Oregon (UO)

 

Clinical and Translational Services 

 

Clinical and Translational Research Core Services

  • Study coordination, education, career development, and investigator support 

Oregon Health & Sciences University (OHSU)

Note: The University of Oregon's core facilities are supported by the Office of the Vice President for Research and Innovation and are available to researchers from UO, other academic institutions, and industry partners. Each facility provides training opportunities and expert consultation in addition to access to state-of-the-art instrumentation. 

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