The Integrated Genomics Lab (IGL) provides a range of genomics services. These include nucleic acid isolation, qPCR, and sequencing library preparation for bulk RNA and DNA and for single-cell RNA-seq using the 10x Genomics Chromium iX. Sequencing is done using either a NovaSeq 6000 or a NextSeq 2000. The IGL also offers alignment of bulk RNA sequencing data and single-cell RNA-seq data. In addition, the IGL provides an oligonucleotide ordering service through IDT and a cell line authentication service.

Core facility that provides the following services: Analytical flow cytometry service, Cell sorting service, Flow cytometry data analysis service, Grant preparation support service, Flow cytometry instrument training, Flow cytometry consultation service. The OHSU Flow Cytometry Shared Resource (FCSR) has operated as a core resource for OHSU Knight Cancer Institute members since 1996 and provides advanced flow cytometry instrumentation, technical expertise and technical services. The FCSR also provides training in data interpretation, experiment design and routine operation to researchers, offering an additional cost-saving option of doing some of the work themselves. Finally, this resource saves valuable investigator time by analyzing specimens and preparing them, if needed.

Core services including ensurance that purified proteins and other biomolecules of interest are uncompromised in terms of their structure and stability. Facilitates analyses of catalytic activities and functional interactions.Examines thermodynamic and kinetic parameters for association between proteins and small molecules.Facilitates hypothesis generation through coalescence of experimental data and computational modeling.Assists in setting up protein crystallization assays.

Core facility that provides the following services: NMR instrument training. A facility that uses a state-of-the-art NMR spectrometer to verify or determine the structure of organic molecules. Housed in the Department of Physiology and Pharmacology, it is designed to exploit the power of designed small molecules as probes of protein and cellular function and to provide the foundation for the development of prototypic therapeutic agents.

Core facility that provides the following services: Clinical specimen processing, Genetic analysis services, Eppstein Bar Virus (EBV) transformation of B-Lymphocyte cells, Sample storage. The OCTRI Core Laboratory is specifically designed and equipped to perform both basic and specialized research assays and sample processing in support of translational research studies and trials. Laboratory staff have extensive experience in the performance of a wide variety of analytical and genetic based assays and procedures.

Transgenic Mouse Models Core laboratory (TMM) is a structural unit of the OHSU Shared Resource Program and is supported by this program and the Knight Cancer Institute at OHSU. The Transgenic Core was established within OHSU in 1994 in response to a growing interest and need for this important technology of many scientists and physicians among different faculties of OHSU. There has been exponential growth of transgenic mouse projects at OHSU with over two hundred fifty unique transgenic and knockout mouse lines produced during the past 17 years. Moreover, the genetically modified mice generated by OHSU''''s Transgenic Core are successfully used by investigators within the USA and other countries. Currently the TMM supports 27 grants from NIH and other funding agencies. Service fees include: 1) Purchase of virgin C57BL6/J or B6xDBA-2F1 females (donors of oocytes). 2) Superovulation of the virgin females. 3) Microinjection into 250-300 C57BL/6 or B6xDBA-2 zygotes. 4) Transplantation of the microinjected embryos into pseudopregnant recipient females. 5) Animal housing charges for recipients and their offspring until weaning. 6) The production of 3 guaranteed transgenic founders. TgMM does not guarantee expression of the transgene. Service fees do not include: 1) Animal housing charges for litters after weaning. 2) Ear/tail tissue collection for DNA isolation for genotyping. 3) Health testing of the foster mother. 4) Shipping charges. Additional Services: According to the customers'''' request, TgMM can purchase and use other mouse lines for the generation of genetically modified mice. Moreover, TgMM can tag, collect tail samples, extract DNA and genotype the offspring by PCR. For this purpose the animals can be housed in our colony beyond the usual 3 weeks (weaning age). These additional services will be charged as extra fees, including the extra costs for the cage(s) per diem.

Provides in vivo imaging technology to evaluate anatomy, tissue function, cellular and molecular phenotype, blood/fluid flow, metabolism and to assess pharmacokinetics and stem cell function in small animal models.Offers spatial resolution, temporal resolution, tissue differentiation, sensitivity for contrast agent, and performance of contrast agents. Services include MicroPET/SPECT/CT imaging,Ultra-high frequency small animal ultrasound imaging,Biophotonics imaging.

Core facility that provides the following services: Protein identification and partial sequencing, Determination of whole protein mass, Targeted SRM analysis of known proteins, Protein quantitation assay, Gel electrophoresis. The OHSU Protemics Shared Resource facility was established to make state-of-the-art mass spectrometry based protein analysis analytical capabilities available to the biomedical research community at OHSU.

Provides RNA-sequencing for gene expression analysis, DNA resequencing for single nucleotide polymorphism discovery, DNA resequencing for copy number variation discovery, ChiP-sequencing for promoter analysis, DNA methylation analysis, De novo sequencing for unique genomes, Sequence capture service. Offers sequencing including genome resequencing, transcriptome analysis, miRNA analysis, and prometer analysis via ChIP-seq.

Core facility that provides the following services: Histology tissue and staining services, Immunohistochemistry staining service. The Histopathology Shared Resource is a College of American Pathologists (CAP) certified and Clinical Laboratory Improvement Amendments (CLIA) accredited core facility that provides investigators with tissue-based services fundamental to the progress of basic, translational and clinical research. The mission the Histopathology Shared Resource (HSR) is to: 1. Provide investigators with histology services critical for the progress of biomedical research involving studies on research animal and human tissues These services include cryostat sectioning, paraffin- embedding, cell pellet and cytospin preparation, microtome-sectioning, histochemical staining and immunohistochemistry. 2. Provide investigators with consultation and education in regard to best use of histopathology services research protocols, safety issues, and IRB application.

Core facility that provides the following services: mRNA expression profiling service, RNA/DNA sample quality assessment, Array hybridization, processing and assay quality control service, Sample amplification and labeling service, Array data preparation and management, RNA/DNA processing service, Basic data analysis, RNA isolation service, qPCR services, Small genome focused panels on Ion Torrent PGM, RNA sequencing service, Copy number variation analysis, DNA genotyping services, DNA methylation analysis service, RNA expression analysis, Single-nucleotide polymorphism analysis. The OHSU Gene Profiling Shared Resource (formerly the Gene Microarray Shared Resource) functions as a full-service genomics facility serving research scientists and clinicians with services for RNA expression profiling and DNA variation analysis on two microarray platforms, Affymetrix and Illumina and on Applied Biosystems QuantStudio real-time PCR system. We are also now able to provide expression profiling and genome analysis services using Ion Torrent PGM sequencer. Support for RNA isolation and RNA/DNA quality assessment also available.

Provides highly sensitive elemental quantification, including sample preparation, data analysis, and experimental guidance, through Inductively Coupled Plasma Mass Spectrometry (ICP-MS) technology.

Provides access to tools for imaging with short lived radionuclides, data analysis and is integrated with campus centers SARIC and nuclear medicine clinic for quantitative imaging of these tracers in vivo that provides spatial and temporal data in order to improve our basic understanding of biochemical pathways, disease processes and help select personalized treatments that enhance clinical care. Highlights of our center include On-campus capacity to develop and produce radiopharmaceuticals to address specific research questions using in-vivo, real-time imaging;PET/CT, SPECT/CT (and soon PET/MRI) imaging capability to quantify organ perfusion, assess metabolic pathways, receptor function and density, and measure pharmacodynamics.Applications are directed toward range of models, ranging from small animals to non-human primates, to humans.

Core provides designing studies and developing statistical analysis plans in clinical trials, clinical and community based intervention studies, laboratory experiments, and observational studies.Provides expertise in traditional and modern statistical methods.Can help with trial design and analysis, epidemiologic analysis, sample size and power, high dimensional data analysis, risk prediction, complex survey analysis, time-to-event and longitudinal models, and statistical simulation,data management and wrangling, analytic variable coding and data set creation, research database design, data visualization, manuscript preparation, statistical programming, and much more.

Core facility that provides the following services: Mass spectrometry services, Mass spectrometry and HPLC sample preparation and data analysis, High performance liquid chromatography services. This resource is available at OHSU for the analysis of small molecules such as drugs and drug metabolites, neurotransmitters, fatty acids and biologically active metabolites of fatty acids, steroids, and natural products . The BSR provides open access to a laboratory where users can prepare and analyze their own samples by HPLC, GC/MS or LC/MS on equipment maintained by Core personnel. In addition, samples can be submitted for complete analysis by Core staff and the Director and Associate Director are available for assay development assistance.

Provides confocal image analysis and presentation training, microscope training, microscope access service, deconvolution training, super resolution imaging and training service. Offers research scientists access to high-end instrumentation for fluorescence microscopy. Offers support with image acquisition, processing, analysis and presentation.

Core facility that provides the following services: Electronics shop access service, Chemistry lab access service, Human subject preparation room access, Animal preparation room access, Mock scanner access, MRI data handling service. The Advanced Imaging Research Center (AIRC) at Oregon Health & Sciences University specializes in generating novel Magnetic Resonance (MR) techniques and technologies for the advancement of biomedical research. The AIRC at OHSU has as its basic mission the advancement of medical imaging. With this charge it has become a center for cutting-edge research in imaging science. It is a research facility independent of existing departments at OHSU.

Core facility that provides the following services: Data storage service, Tape backup service, Server set up and hosting, Cluster slice service, Application set up and hosting, Database design, hosting and maintenance, ACC consulting service, Alternative to cloud data storage service. The mission of the Advanced Computing Center (ACC) at OHSU is to meet the advanced computing needs of the OHSU research, academic, and administrative community by providing a scalable set of advanced computing services that augment and supplement no-cost core services provided to the OHSU Enterprise by the Information Technology Group. General services offered include an on call systems and database admin available after hours.

DNA sequencing & fragment analysis is accomplished with our state-of-the-art, Applied Biosystems 3130xl, capillary fluorescence instrument. Several levels of service are available to match your needs and finances. We are happy to consult on your sequence assembly and analysis or other data processing, informatics, and database needs as well.

The Multiscale Microscopy Core at OHSU is a state-of-the-art electron microscopy core that provides services and training to academic and corporate users.

The BBC provides experimental design, grant support, data analysis, manuscript preparation, and individualized training falling in two main categories: 1) 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; and 2) Biostatistics such as statistical genetics, longitudinal, survival, and high-throughput/high-dimensional omics data analysis. The BBC's integrated structure comprising of experts with diverse training permits analysts to work together on projects that require multiple skillsets. Each analysis is customized to best fit the needs of the project and investigator.

The KCVI Epigenetics Consortium assists investigators analyzing epigenetic regulation by taking advantage of constantly evolving technologies and high throughput sequencing.

Current services available include:

DNA Methylation
-Whole Genome Bisulfite Sequencing (WGBS)
-Reduced Representation Bisulfite Sequencing (RRBS)
-Illumina TruSeq Methyl Capture EPIC Library Prep
-Targeted Allelic Bisulfite Sequencing (Sanger based)

Chromatin Interactions
-Chromatin Immunoprecipitation Sequencing (ChIP-seq) -Assay for Transposase Accessible Chromatin Sequencing (ATAC-seq)

Extractions for use with Core Services
-DNA
-RNA

Bioinformatic analysis of epigenetic datasets




We closely collaborate with the Massively Parallel Sequencing Shared Resources and Gene Profiling University Shared Resources at OHSU.