The University of Washington Mouse CRISPR Core (UWMCC) is a cost center administered through the Department of Comparative Medicine at the University of Washington (UW), Seattle, WA. The UWMCC is a full-service facility offering rapid, precise and economical generation of novel transgenic mouse models using CRISPR/Cas9 gene editing technology. Our standard service includes consultation, design, testing, prep, mouse embryo microinjection, and genotyping all at a competitive price point. The UWMCC is a joint collaboration utilizing 15 years of gene-editing experience by the UW Transgenic Resources Program, the UW Institute for Stem Cell and Regenerative Medicine, and the Vector and Transgenic Mouse Core of the UW Diabetes Research Center.

The Transgenic Resources Program (TRP) is a core facility that creates transgenic and gene-targeted mice using pronuclear microinjection, targeted ES cell microinjection, and CRISPR-Cas9 gene editing. The TRP also offers mouse rederivation services to create specific pathogen free mice or to revive cryopreserved mouse lines. Additionally, embryo and sperm cryopreservation services are available to provide long-term storage of valuable mouse strains or stocks. Our facility is available to all University of Washington investigators and outside institutions.

Magnetoencephalography facility focusing on children. Equipped with MEGIN TRIUX Neo system with helium recycler, MAGSTIM EEG data acquisition system, Tucker-Davis Technologies RZ6 for stimulus generation, Epson Home Cinema 3200 for video projection, custom video recording system with 4 cameras, Eyelink eyetracker, and Polhemus 3D digitizer.

The Preclinical Research and Translational Services (PRTS) Core at the University of Washington (UW) is a collection of individual core facilities that provide support for both internal (UW) and external (outside of UW) collaborators, researchers, and scientists.

Managed by the Department of Comparative Medicine, the PRTS Core provides in-life services including the Transgenic Resources Program (TRP), In Vivo Services (IVS), the Gnotobiotic Animal Core (GNAC), the Biosafety Level (BSL-3) Facility, and the Patient Derived Xenograft (PDX) Core, as well as pathology support by the Histology and Imaging Core (HIC) and the Comparative Pathology Program (CPP).

The Gnotobiotic Animal Core (GNAC) at the University of Washington (UW) is a core facility started in 2014 and managed by the Department of Comparative Medicine. Located in the UW Health Sciences Center, the GNAC is open to investigators with research needs to create or maintain mice free of any microorganisms (germ-free), or with a known population of microorganisms (gnotobiotic). Our facility is available to all University of Washington investigators as well as outside institutions.

The Histology and Imaging Core (HIC) provides histology, immunohistochemistry, imaging, quantitative image analysis, and pathology consultation services. We employ extensive experience, expertise and state of the art high-throughput instrumentation across all platforms in our facility. This core is open to all investigators, including; UW and their affiliates, commercial and not-for-profit biotechnology companies, and other academic institutions. Through our partnership with the Comparative Pathology Program (CPP) we have access to experienced comparative pathologists who are available for research consultation and collaboration.

The In Vivo Services (IVS) Core provides mouse colony management at the UW. IVS staff will oversee the maintenance, breeding, weaning, identification, and record keeping of your mouse colonies to free up the limited and valuable time of your laboratory personnel. In addition, the IVS Core offers an array of technical services performing procedures such as sample collection, sample administration, metabolic testing, behavioral assays, and testing of drug compounds in rodents. Our facility is available to all University of Washington investigators and outside institutions.

The Sanford Burnham Prebys Cancer Metabolism Core provides a unique service for the analysis of metabolism, offering both metabolite quantification and stable-isotope tracing methodology, centered around gas chromatography-mass spectrometry (GC-MS). We offer GC-MS analysis of polar metabolites (TCA cycle, glycolysis metabolites and amino acids), short chain fatty acids, fatty acids and cholesterol, sugars and sugar-phosphates. As well as cells, we can also analyze tissues, tumors, serum or culture medium as necessary. We also have available a YSI 2950 analyzer for measurement of glucose, lactate and glutamine in medium samples. We collaborate closely with Core users and can provide in-depth advice on the direction of metabolic experiments, as well as the interpretation of results.

The Sanford-Burnham Proteomics Facility provides state-of-the-art mass spectrometry-based proteomics services with methods tailored to the needs of scientific investigators for routine mass spectrometric analysis of peptides and proteins, identification of novel proteins, characterization of post-translational modifications, and quantitative proteomics analysis of simple to complex biological samples. The facility identifies, validates and develops new methods designed for the characterization and identification of biologically important proteins. It also supports users with software applications and development, data analysis and experimental design of proteomics studies. The facility is continuously expanding its capabilities in large-scale differential proteomics analysis and phosphoproteomics for unbiased discovery of potential biomarkers and mapping protein profiles. We provide proteomics services to Sanford-Burnham scientists as well as outside non-profit and for-profits organization on a fee-for-service basis.

A flow and mass cytometry core for the University of Maryland system.

The Protein Analysis Lab provides multiple technologies for the purification and analysis of proteins, peptides and small molecules. Mass Spectrometry is used for protein identification, quantitative global protein profiling and targeted quantification of peptides and small molecules. HPLC techniques are used for analysis or purification of biomolecules and include ion exchange, hydrophilic interaction, size-exclusion, and reversed phase chromatography.

SBMRI Proteomics Facility provides state-of-the-art mass spectrometry (MS)-based proteomic services for analysis of peptides, synthetic compounds, carbohydrates and proteins by facilitating protein identification, the qualitative and quantitative characterization of post-translational modifications, plus quantitative and differential proteomic profiling of low-complex biological samples. Facility staff regularly identifies, validates, develops, and implements new methodologies for identification, quantification and characterization of biologically important proteins. Such approaches can support a mechanistic understanding of cancer and other life threatening diseases, as well as identify new therapeutic targets and diagnostic biomarkers.
The Proteomics Facility also supports users with grant write-up, proteomics software applications, data analysis, and experimental design of proteomic studies. The facility is continuously expanding its capabilities in large-scale differential proteomics analysis and in phosphoproteomics (and other PTMs) for discovery of potential biomarkers and mapping protein profiles.

State-of-the-art imaging and analytical services:
- The facility can perform in vivo non-invasive luminescence and fluorescence imaging for xenograft tumor growth and metastasis studies.

- Analytical equipment supports complete blood cell counts (CBC) and analysis of serum components revealing metabolic or organ stress from small samples of mouse blood.

The animal facility provides housing for specific pathogen free (SPF) rodents, frogs and Zebrafish. Trained animal care technicians provide expertise in animal husbandry, transgenic and knockout mouse breeding colony maintenance and assistance with routine technical procedures.

Our animal research program is accredited by AAALAC International (the Association for Assessment and Accreditation of Laboratory Animal Care International. Participating in the AAALAC accreditation program and meeting their rigorous standards demonstrates our commitment to humane and responsible animal research and our dedication to good science

Variety of protein production services including cloning, expression optimization, development of protein purification protocols, and protein preparation. E. coli, insect (SF9, baculovirus) and mammalian (293) systems are available for protein expression. Our analytical services are focused on biophysical characterization of structural and functional properties of proteins in solution, under native, non-denaturing conditions. We can perform quality control of protein samples (folding, stability, aggregation, etc.); characterize protein conformation and shape in solution; and measure protein binding to proteins, peptides, small molecules and other ligands (including determination of equilibrium (Kd) and kinetic rate (kon, koff) constants, stoichiometry, binding enthalpy and entropy).

The Stem Cell Core Facility (SCCF) at the Burnham Institute provides scientist’s within the Sanford Stem Cell Consortium an area to conduct their research that is devoted entirely to Human stem cells and that is conducive to collaborative partnerships.
The SSCF also provides researchers with a source of both approved and non-approved embryonic stem cell lines, induced pluripotent stem cell’s, cell-line profiling services, reagents, and instruction for all areas regarding the maintenance, differentiation and manipulation of stem cells. The SCCF has also just completed a CIRM funded renovation and expansion that allows us to increase greatly the products and services that we can offer the members of the Consortium.

The facility provides microarray-based global analysis of gene expression in human, mice and rats using an Illumina platform. Starting with investigator RNA samples, the facility confirms RNA quality, and then performs microarray analysis as well as initial data analysis. Array data are returned to the investigator, and if desired, also passed on to the Informatics and Data Management facility for more detailed analysis. Both mRNA and miRNA profiling are available. Quantitative real-time PCR (Q-PCR) service is predominantly SYBR green-based analysis, but hybridization probe (e.g. TaqMan) approaches are supported. Starting with RNA, the facility will utilize primers from investigators, or design custom primers and perform Q-PCR. The facility provides control primers and assists with experimental design, as well as providing basic relative quantitation analysis. Q-PCR analysis in the facility can also provide gene, RNA, or viral copy number data.

The Histopathology Core Facility provides standard and customized research specific histology services including tissue processing, fixed and frozen sectioning. The Facility also offers routine and special histological stains as well as immunohistochemistry and immunofluorescence. The Facility maintains and provides training for several pieces of common use equipment, such as, paraffin microtome, cryostat, and a cytospin. Training is also provided for basic histological techniques such as, perfusion and tissue collection. Finished slides are returned to the researcher for evaluation, or they may be scanned in our Aperio Scanscopes that allows digitizing of slides for archiving, and electronic distribution/remote analysis of histology slides, and offer, powerful image analysis tools. Scanning of fluorescent slides is also available.

The Cell Imaging Facility broadly supports research programs by providing access to sophisticated microscopes for digital imaging, as well as training, assistance and guidance, helping scientists from any institution on a “first come-first served” basis.

It offers expertise, training and assistance in advanced biological microscopic imaging techniques and use of complex image processing software, use of well-maintained, aligned, and calibrated microscopic equipment, and troubleshooting of equipment and experimental problems.

The Microarray Facility provides services and support for researchers doing RNA expression, miRNA expression, transcription factor binding and other assays utilizing microarray technology. Services are available to all researchers at the Institute as well as external institutions and collaborators. The facility supports the Affymetrix, Agilent, and Exiqon platforms for RNA and miRNA measurements as well as an in-house spotter to fabricate custom oligo arrays. Also available is the Fluidigm Biomark which can run single cell expression analysis.

Core dedicated to the protocol driven collection, analysis, and reporting of behavioral data using a blend of classic and innovative assays. Supports neuroscience, psychology, pharmacology, genetics, cancer, and development by providing advanced tools and expertise for the precise measurement and interpretation of behavior.

The BRI Biorepository is responsible for the collection of samples from research participants, sample processing, storage, and sharing. We currently store samples from participants with a wide range of autoimmune diagnoses and healthy controls.

The Genomics Core provides resources to BRI and external investigators for genomics analysis, from sample processing through data generation, as well as basic bioinformatics analysis, provided by our Bioinformatics Core Team. Currently available technologies focus on Illumina RNA and DNA sequencing. RNA-seq can be performed from a variety of sample types, including purified total RNA, cell populations (including low input samples of 50-1000 cells), or single cells (either plate-sorted rare populations or high-throughput 10x single-cell analyses). DNA-seq pipelines can also be performed, including bulk CUT&Tag/CUT&RUN, and ATAC-seq and single cell ATACseq and multiome capture. Custom prepared libraries can also be submitted for sequencing.

The Core laboratory houses three Illumina sequencers, two NextSeq2000 instruments and a Miseq, plus a 10x Chromium X and a 10x CytAssist. The Chromium X is able to run GEM-X assays on fresh cells and Flex assays on fixed cells. The CytAssist works to perform spatial profiling using Visium HD technology.

Additional equipment includes a ThermoFisher Kingfisher Flex, for extracting nucleic acid from a variety of sample types using magnetic bead technology with a throughput of up to 96 samples. Two Qiagen QIAcube Connect instruments automate extraction of nucleic acid using spin column technology. Ancillary equipment for sample processing includes a Formulatrix Mantis Liquid Handler, an Agilent TapeStation 4200 (to measure RNA/DNA integrity and size), and a Tecan NanoQuant (for high throughput sample quantitation).

The Human Immunophenotyping (HIP) core at the Benaroya Research Institute (BRI) provides access to cutting-edge technologies and services enabling study of human immune-mediated diseases.

We offer expertise in human immunology along with innovative assays and state-of-the-art technology. We specialize in robust, high-parameter single-cell assays utilizing conventional, spectral, and mass cytometry (CyTOF), which can be paired with sophisticated genomic and bioninformatic analyses through our connections with other outstanding BRI cores. Other services include, but are not limited to, cell sorting, short-term in vitro assays, DNA/RNA extraction, qPCR, and ELISA or multiplex protein analysis (Luminex).

We tailor our support to meet the unique needs of each researcher. A full spectrum of services is available, from guidance on study design and training on new technologies through to execution, data analysis and interpretation. The HIP core serves investigators from BRI and Virginia Mason Medical Center (VMMC) as well as other institutions, including both non- and for-profit organizations.

The Cell and Tissue Analysis (CATA) Group at the Benaroya Research Institute offers an extensive array of flow cytometry, imaging, and histology resources for both BRI investigators as well as external research entities.

Spread over three floors at the BRI, the CATA Group strives to provide researchers with consistent and dependable access to cutting-edge technologies. With expertise in the fields of imaging, histology, and flow cytometry, we seek to not only offer the physical space and machines necessary to carry out your work but also critical support through the whole process, from hands-on training to experiment design and data analysis.