Research Cores & Services
Yale’s Core Research Facilities provide Yale researchers access to state of the art scientific instrumentation, highly trained staff, and extraordinary consultants and specialists with the intent to keep Yale’s scientific research at the cutting edge. Within the School of Medicine, there are a number of services that make available research resources for internal investigators. Many of these resources are available to external investigators on a core by core basis.
Research Cores & Services
Microscopy and Imaging Cores
- 3D Collaborative for Medical Innovation (3DC)
The 3D Collaborative for Medical Innovation (3DC) provides engineering and 3D printing services to Yale researchers. While the 3DC specializes in projects based on medical imaging data, we can support other projects as available. Engineering services include medical imaging data segmentation, the creation and/or modification of digital anatomical models, 3D analysis of digital anatomical models, computer aided design (CAD) of medical devices and/or test devices, preparation and/or deployment of 3D digital models into extended reality, or other similar tasks.
The 3DC offers 3D printing of digital files using stereolithography, a resin-based printing technology. The 3DC can modify and optimize your files for 3D printing. Engineering and biocompatible materials are available.
Contact: Alyssa Glennon
- CCMI Confocal Microscopy
Technology: Multiple confocal microscopy systems
Operational Model: Training and for user access to seven confocal systems including Airyscan, STED, Swept Field, Light Sheet and Super Resolution Microscopes. Software programs from multiple vendors are available for post-acquisition analysis including fluorescence deconvolution, 3D rendering, measurements of time lapse data and fluorescence co-localization.
More information about CCMI Confocal Microscopy
Contact: Al Mennone
(203) 785-3793- CCMI Bio-Electron Microscopy (EM)
Technology:
- Cell and tissue sample processing, embedding in resin for TEM
- Ultramicrotomy of plastic sections · Cryo-sectioning and immuno-gold labeling (Tokuyasu method)
- Immuno-electron microscopy · Transmission electron microscopy and digital imaging
- Scanning electron microscopy · Electron tomography for resin embedded samples (single/dual tilt series)
- Focused ion beam SEM sample preparation and 3D data collection (FIB-SEM)
- Training on operating various electron microscopes and sample prep instrument
- Consultation and assistance in experimental design, grant application and publication
Operational Model: staff-provided sample preparation and imaging, or training for independent imaging
More information about CCMI Bio-Electron Microscopy
Contact: Xinran Liu, PhD
(203) 785-4050- CINEMA
Services: Microscope imaging center: Imaging technologies (microscopes)-TIRF, Spinning Disk, STED & SIM
- Positron Emission Tomography (PET) Center
Services: PET scans and related services (radiosynthesis, metabolite analysis; ligand development, PK studies).
- Yale MR Image Res Center (MRRC)
Services: All of the resources necessary for integrated studies of human brain function including research magnets and personnel for electrophysiological (1 dedicated EEG room) and psychological testing (3 behavioral testing rooms), computing, and image and data analysis. Dedicated to research activity.
- Stem Cell Imaging Core
- The Cell Imaging Core is equipped with a Leica TCS SP5 Spectral Confocal Microscope, 405UV with acousto-optical filter, acousto-optical beam splitter, prism spectrophotometer detection and controlled environment cell culture chamber. The Core also has a wide field Leica DMI6000 B inverted fluorescence microscope with adaptive focus control for phase contrast, DIC and epi-Fluorescence. There is also an image processing workstation for deconvolution and/or 3D rendering of images.
Operational Model: Training and instrument access
- Microscopy Core
Services: Cryo Microscopy & Imaging Core includes a cryomicrotome, and ultramicrotome, a Zeiss electron microscope, a Zeiss Axiophot epifluorescent photomicroscope and a Zeiss laser scanning confocal microscope. Technical staff provide support for users of this facility. Cryo Microscopy - Freeze a tissue sample, slice, mount, stain and return to customer. Usage of cryostat, cut cryostat sections, slided that are used for the cryostat
- Cardiology Confocal Microscope Facility Ultraview Vox System
- YCVRC Confocal systems
1. Leica TCS SP8 Confocal Laser Scanning Microscope (upright) (GSF 754)
Objectives: 10X, 25X (water), 63X (oil). HyD and PMT detectors. Conventional and resonant scanners. 5 Laser lines. Integrated FRAP/FRET module. Lightning Super-resolution module.
2. Leica TCS SP8 Confocal Laser Scanning Microscope (inverted) with incubator (GSF 729)
Objectives: 10X (dry), 20X (dry), 40X (oil), 63X (oil). HyD and PMT detectors. Conventional and resonant scanners. 4 laser lines. Integrated FRAP/FRET module. Lightning Super-resolution module. Ludin box incubator with air/temperature control.
3. Leica TCS SP5 Confocal Laser Scanning Microscope (GSF 754)
Objectives: 10X, 20X, 25X (water), 40X (water), 63X (oil). PMT detectors. Ludin box incubator with temperature control.
4. Perkin Elmer 5-Laser Spinning Disk Confocal (GSF 729A)
Five Lasers lines. Photokinesis unit for FRAP and photoswitching experiments.
Objectives: 4X, 10X, 20X, 40X, 60X (oil) and 100X (oil).
Nikon Ti-E Eclipse inverted microscope equipped with Perfect Focus (auto focusing system), motorized XY stage and Nano Focusing Piezo Stage
Operational Model: Training and instrument access, open access to Yale or non-Yale users.
Contact:- Confocal Manager: Dongying (Tony) Chen, dongying.chen@yale.edu
- Laboratory Manager: Yogita Verma, yogita.verma@yale.edu
- FIB-SEM Collaboration Core (F-SCC)
- Technology:
At the forefront of volume Electron Microscopy, F-SCC welcome your collaboration to drive discoveries in life science to a whole new level using the state-of-the-art enhanced FIB-SEM technology and its unparalleled pipeline for large volume 3D imaging with nanometer isotropic resolution.
Operational Model:
Investigators prepare a project description (according to Collaboration Guidelines), then meet with F-SCC directors to review details. The discussion will facilitate a joint assessment on how well the platform and pipeline match up with the investigator’s project and discoveries. Submitted samples will be prepared and imaged by the trained staff scientists in F-SCC.
Contact: Song PangPhone: 203-785-4484.
Flow Cytometry and CyTOF
- Yale Flow Cytometry Facility
- Technology: Flow cytometry analyzers and fluorescence activated cell sorting, and Amnis Imagestream Imaging Flow Cytometer, Luminex, FlowJo Site License access
Operational Model: Provides training and access for Flow Cytometry Analyzers and staff-assisted Cell Sorting; PBMC isolation and cryopreservation; Plasma or serum purification; Luminex assays, data acquisition & analysis (with user provided kits); Immunofluorescence surface or intracellular cell staining, analytic data acquisition and analysis.
Contact: Ann Haberman, ann.haberman@yale.edu
(203) 785-7349 - CyTOF
- Technology: Analysis of cells with a stable heavy metal isotope using time-of-flight atomic mass cytometry and imaging mass cytometry (IMC). Core maintains a repository of well-characterized metal conjugated antibodies, metal labeling reagents, metal-conjugated anti-fluorochrome antibodies (e.g. anti-FITC).
Operational Model: Staff assisted access
Contact: Ruth Montgomery, PhD Ruth.Montgomery@yale.edu
(203) 785-7039
Genomics and Proteomics Cores
- Yale Center for Genome Analysis
Technologies: Next-Gen Sequencing with multiple platforms (Illumina, Pacific Biosciences, 10X Genomics), Bioinformatics and microarrays for expression analysis, genotyping, miRNA and methylation analysis
Operational Model: Staff-provided services for Next-Generation Sequencing, Bioinformatics and Microarrays
More information about Yale Center for Genome Analysis
Contact: ycga@yale.edu
(203) 737-3031- Mass Spectrometry and Proteomics
Technology:
- Basic Protein ID from gel bands
- Protein ID from complex solution
- Protein Posttranslational Modification (PTM) identification
- Protein profiling and quantitation (Labeled Free Quantitation, iTRAQ, TMT, & SILAC)
- Intact Protein Determination
- High Resolution (HR) MS for small molecule
- Targeted Proteomics (PRM)
- Metabolomics Biomarker Assay (utilizing Biocrates p180)
Operational Model: Staff-provided and Open Access
More information about Mass Spectrometry and Proteomics
Contact: TuKiet Lam
(203) 785-5086- DNA Sequencing
Technology: Sanger sequencing services including individual samples, plated samples, PCR purification, fragment analysis, RT-PCR, and DNA and RNA QC Analysis
Operational Model: Staff-provided service
More information about DNA Sequencing
Contact: Amy Blanchard
dnasequencing@yale.edu
(203) 737-2566- Oligo Synthesis Resource
Technology: Oligos including modified oligo and plate-based formats, custom cloning, RNA and methylated RNA, mixed bases, and purification
Operational Model: Staff-provided custom synthesis of oligonucleotides
More information about Oligo Synthesis Resource
Contact: Joe DeLuca
oligos@yale.edu
(203) 737-2541- Functional Genomics Core
Services: ShRNA and CRISPR/Cas9 screens in human and mouse cells. Resources include pooled libraries for screening, consultation and guidance in performing screens, and bioinformatics support for analysis of screening data. The core houses genome-wide collections of shRNA constructs and full length human ORF cDNAs that are available as individual constructs.
- YSCC Genomics Core Service
The YSCC Genomics Core Service provides DNA sequencing services, Transcriptome analysis (RNA-Seq), Small RNA discovery (smRNA-Seq), Gene regulation & epigenetic analysis (ChIP-Seq), Customized sequencing per user design and single cell genomics with Fluidigm C1 IFCs
Structural Biology and Biophysics
- Keck Biophysical Resource
Technology: Resources to study oligomeric state of biomolecular assemblies, as well as thermodynamics and kinetics of macromolecular interactions using:
- light scattering
- dynamic light scattering detector (DLS)
- isothermal microcalorimetry (ITC)
- surface plasmon resonance - BiaCore biosensor (SPR)
- stopped-flow spectrofluorometer
- Spectrofluorometer: PTI-QuantaMaster
- Asymmetric flow Field-Flow Fractionation
- Fluorescence plate reader
- CD - spectrophotometer
Operational Model: Training and instrument access
More information about Keck Biophysical Resource
Contact: Ewa Folta-Stogniew
(203) 737-4387- Macromolecular X-ray Crystallography
Technologies: Protein characterization (MALS detector, Nano isothermal titration calorimeter), robotic crystallization preparation, crystallization imaging and growth monitoring, X-ray diffraction data collection, data processing and structure determination software.
Operational Model: Training and instrument access and staff-provided service
More information about Macromolecular X-ray Crystallography
Contact: Jim Murphy
(203) 906-5759- Macromolecular Structure Analysis Consultation Core
- Expertise Available
- Develop new methods for quantitative analysis of experimental charge density maps and electrostatic potential maps
- Analyze molecular dynamics trajectories and other large-scale structural analysis
- Perform and/or advise on many software packages to generate publication quality illustrations of high-resolution macromolecular structures
Services- Project evaluation:
- Project feasibility effort provided for one day per new project, free of charge.
- Initial meeting to understand project goal and evaluate any available data.
- Summary recommendations provided in short report, including an estimate of the amount of time needed for further support on the project.
- Project completion:
- Work begins upon written acceptance of proposal, or after additional discussion and modification.
- Time is tracked on research effort and communications about the project, including meetings, discussing methods, preparing reports, and writing results.
- Project billing:
- Payment can be included as a percent effort on proposals, or at the daily rate.
Contact- Contact Jimin Wang, PhD, Research Scientist in Molecular Biophysics and Biochemistry
- Jimin.wang@yale.edu
- Room 341, Bass Center for Molecular and Structural Biology
- 203-432-5737
- Publications
Animal Research Cores
- Yale Genome Editing Center
Technologies: YGEC creates genetically engineered mice via CRISPR/Cas genome editing, gene targeting via homologous recombination in ES cells, and traditional transgenic mouse technology. YGEC also cryopreserves sperm or embryos of inherently valuable genetically altered mouse strains. Assisted reproduction technologies include strain reanimation or rescue via in vitro fertilization and/or embryo transfer.
Operational Model: Staff-provided services
More information about Yale Genome Editing Center
Contact:
- Tim Nottoli (203) 737-4325 to discuss constructs for creating transgenic mice, gene targeting and genotyping
- Xiaojun Xing (203) 785-6923 to discuss microinjection, zygote electroporation, IVF, cryopreservation and rederivation.
- Yale Zebrafish Research Core
Technology: Expert resources to create transgenic zebrafish and provide assistance in phenotyping them.
Operational Model: Staff-provided service
More information about Zebrafish Phenotyping Core for Precision Medicine
Contact: Andrew Prendergast
(203) 843-0870- Yale Animal Resources Center
Animal housing husbandry complete veterinary services on the care and use of animals.
- Center for Precision Cancer Modeling
In vivo pharmacological evaluation of anti-cancer therapeutics. Services include efficacy, toxicology, pharmacokinetics, pharmacodynamics and imaging studies
- In Vivo Imaging Facility (IVI)
Resources including staff support for a two-photon laser scanning microscope and surgical preparation area to perform time-resolved intravital imaging of rodents.
- Yale Translational Research Imaging Center (Y-TRIC)
Small and large animal CT, SPECT-CT and ultrasound. Small animal laser Dopler flow. Large animal fluoroscopy. Pre- and post-operative animal care assistance associated with animal surgery.
More information about Yale Translational Research Imaging Center
- O'Brien Kidney Center-Renal Physiology Core
Provides a variety of services that phenotype kidney function including assessing renal function in small animals at the level of single tubules in vitro and in vivo, the whole kidney, perfusion fixation for histology studies, and the intact organism.
More information about O'Brien Kidney Center-Renal Physiology Core
- Center for IOMIC Flux
The Islet, Oxygen consumption, Mass Isotopomer flux core (IOMIC) measures islet function, oxygen consumption, and cellular metabolic flux
- Automated Complete Blood Counts (Hemavet)
The Core uses a Hemavet veterinary hematology analyzer that provides accurate CBC counts from whole blood of mice, rats, dogs, and humans (research use only).
- Cesium irradiator and x-ray irradiators
Enables irradiations of molecular compounds, cell culture, animal and human tumor cells, and whole animal experiments.
More information about Cesium irradiator and x-ray irradiators
- Comparative Pathology Research Core
Pathology support for animal-based studies to better understand disease processes and their treatment including comparative pathology, histology, necropsy and virology.
- Molecular and Serological Diagnostics
Testing of tissues, cells, feces and environmental samples for veterinary viruses, bacteria, parasites and fungi by PCR and RT-PCR. Biological contaminant testing of samples to be inoculated into rodents is required by IACUC and is free of charge to Yale principal investigators. Testing of mouse and rat sera for rodent viruses and Mycoplasma pulmonis.
More information about Molecular and Serological Diagnostics
- Yale Orthopedics Biomechanics Lab
This lab assesses the biomechanical properties of musculoskeletal tissues, providing services and technical assistance.
Diagnostics Cores
- Genetics Cytogenetics Research
Services include chromosome karyotyping, cell and tissue culture (most organs, both human and non-human sources), fluorescence in situ hybridization, banding techniques (HRB, CBG, GTW, replication, SCE, and others), and advanced array comparative genomic hybridization (aCGH) diagnostics. Types of specimens processed include blood, amniotic fluid, chorionic villus, products of conception, bone marrow, skin and solid tumor samples from clinicians as well as various cell lines and tissues from researchers.
- DNA Diagnostics Lab
College of American Pathologists and CLIA certified laboratory with decades of experience in the molecular diagnosis of genetic disease. We provide testing for cancer predisposition, metabolic and developmental disorders. Provide GeneTests and custom re-sequencing assays.
- Mol Diagnostics
Molecular Diagnostics by PCR and FISH tests including tests for clonal rearrangement, microsatellite instability, chromosomal segment deletion or translocation
- Tumor Imaging Metrics Core (TIMC) and Imaging Support Services
- The mission of TIMC is to provide standardized, longitudinal radiological measurements to evaluate therapeutic responses for clinical trials. TIMC tracks changes in tumor measurements per study protocol, which is essential for clinical trials that use radiological measurements as surrogate endpoints. The system manages these images and takes measurements in a routine and centralized method.
Imaging Support Services, ISS, manages the imaging components of the Yale Cancer Center’s clinical trials from budget and feasibility through close out. Staff reviews sponsor and cooperative group protocols, imaging acquisition guidelines, and imaging manuals to identify standard and non-standard imaging to ensure feasibility. This includes determining the appropriate fees and imaging resources for project completion, completing the image transfer out of PACs to the sponsors for all disease teams, and serving as the primary contact for sponsors and central vendors. ISS also manages the clinical research radiology approvals for non-standard imaging/pricing.
Operational Model: Staff-provided service with MD oversight
Contact: MD Director – Michael Spektor, Staff Manager – Eliot Funai, Support Email – ydrcto@yale.edu
Pathology and Histology Cores
- Comparative Pathology Research Core
Pathology support for animal-based studies to better understand disease processes and their treatment including comparative pathology, histology, necropsy and virology.
- Dermpath Research Histology
Process and Embed Tissue; Cut and Stain, 1st H&E Slide; Additional Cut Unstained Slide; Additional Cut and Stained H&E Slide; Special Stain; Immunohistochemistry; Immunofluorescence; 20X Slide Scan (Delivered on flash drive); 40X Slide Scan (Delivered on flash drive); 20X Slide Scan (PathPresenter-3mo. Max); 40X Slide Scan (PathPresenter-3mo. Max); In-Situ Hybridization (HPV High + Low); Frozen tissue mounting, cutting and staining
Operational Model: Staff-provided service
Contact: Dilgash Mekael, office #: 203-737-4363
- Orthopædic Histology and Histomorphometry Laboratory
The primary service provided is specialized processing, plastic embedding and cutting required for undecalcified tissues and biomaterial implants. Other services provided by this lab include routine paraffin embedding and sectioning, frozen sectioning, routine and special stains and immunohistochemical as well as enzyme histochemical stains. Also, histomorphometrical analyses of bone and other tissues are performed by this lab.
More information about Orthopædic Histology and Histomorphometry Laboratory
- Yale Pathology Tissue Services
Embedding/Sectioning of Tissue, Stain. Tissue Microarray: Construction of Core Master Block, Slides from Tissue Microarray master blocks, Test Array. Antibody Validation, Antibody Titration, Quantification of Protein Expression in Tissue, In Situ Quantification of m-RNA Levels, Index Array Development
Drug Discovery
- Yale Center for Molecular Discovery
Technology: Resources for assay development and high throughput screening with small molecules in biochemical, cell-based and image-based assays (primarily 384-well format). Human CRISPR whole genome library available. Reformatting of samples in 96-, 384- and 1536-well plates. Platereading with a variety of modalities including FLIPR. High throughput image analysis.
Operational Model: Staff-provided service and Self Service Laboratory (subset of instruments)
More information about Yale Center for Molecular Discovery
Contact: Yulia Surovtseva
(203) 737-3271
Machine Shop
- Machine Shop
Technology: Expert, custom services for custom design and fabrication, and repair, as well as tools for loan.
Operational Model: Staff-provided service including on-site and emergency service
More information about the Machine Shop
Contact: Tony DeSimone
(203) 785-4677
Resource Cores
- YSCC/ HESC / IPSC Core Facility
Genome editing service:
- The hESC/iPSC Core provides hESCs and iPSCs genome editing services including single/a few nucleotides replacement, gene knock-out, reporter knock-in using CRSPR/Cas9 technology
- Operational Model: Staff-provided services
- Contact:
- Caihong Qiu: 203-737-7925 project details and design
- Yinghong Ma: 203-785-6673
iPSC generation service
- The hESC/iPSC Core provides services for reprogramming differentiated cells into induced pluripotent cells using non-integration techniques in defined media and feeder-free conditions. The technique can be Sendai virus, episomal vectors or mRNA reprograming. The source cells can be fibroblasts, peripheral blood mononuclear cells or other somatic cell types
- Operational Model: Staff-provided services
- Contact:
- Caihong Qiu: 203-737-7925 for somatic cell types and reprogramming methods
- Jason Thomson: 203-785-6673
hESC/iPSC characterization service:
- Pluripotency tests of hESCs and iPSCs including G-Band karyotype and teratoma formation
- Contact:
- Jason Thomson: 203-785-6673
hESC/iPSC culture training service:
- hESC and iPSC culture training for Novices. It is hands-on training on thawing, maintenance, expansion, and differentiation of human pluripotent stem cells.
- Contact:
- Caihong Qiu: 203-737-7925 for training details and schedule
Reagents and cell line repository service:
- Culture media and essential reagents for hESC and iPSC culture, and live cells or frozen vials of hESCs and iPSCs.
- Contact:
- Jason Thomson: 203-785-6673
Website Links:
- CD34 Cells, Selected PBSC
CD34+ Cells from healthy human donors for use in research
- Tissue Culture Vascular Biology and Therapeutics
Provide well characterized cultures of HUVEC, HECFC Cells, Media, placenta or cord blood, and media component for culturing endothelial cells.
More information about Tissue Culture Vascular Biology and Therapeutics
- Yale University Reproductive Sciences Biobank
Provide the ethical collection, storage, annotation, and distribution of tissue and bodily fluids to support translational research for the field of Obstetrical and Gynecologic pathology.
More information about Yale University Reproductive Sciences Biobank
- FIB-SEM Collaboration Core (F-SCC)
- Technology:
At the forefront of volume Electron Microscopy, F-SCC welcome your collaboration to drive discoveries in life science to a whole new level using the state-of-the-art enhanced FIB-SEM technology and its unparalleled pipeline for large volume 3D imaging with nanometer isotropic resolution.
Operational Model:
Investigators prepare a project description (according to Collaboration Guidelines), then meet with F-SCC directors to review details. The discussion will facilitate a joint assessment on how well the platform and pipeline match up with the investigator’s project and discoveries. Submitted samples will be prepared and imaged by the trained staff scientists in F-SCC.
Contact: Song PangPhone: 203-785-4484.