• DNA methylation profiling
• Protein-nucleic acid association
• Single-cell transcriptomics, immune profiling, and epigenomics
• Spatial transcriptomics
• Bioinformatics analysis
• Scientific support for researchers working on epigenetic and epigenomics

• Illumina NovaSeq 6000
• MiSeq h
• Kodak* Gel Logic 200 Imaging System
• NanoDrop spectrophotometer 1000
• Zephyr
• Chromium controller

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Flow Cytometry Core

The Flow Cytometry Core Facility (FCCF) strives to maximize scientific impact by providing expertise and training in all aspects of flow cytometry and by offering reliable yet cutting-edge instrumentation. The FCCF began as a joint venture between Weill Cornell Medicine and the Hospital for Special Surgery in 2016 and offers expert-operated cell sorting, customer-operated FACS analysis, training for self-operation of FCCF cytometers, and consultation regarding experimental design and data interpretation. These services, alongside cutting-edge, expertly-maintained instrumentation, fulfill the FCCF mission of striving to maximize the utility and scientific impact of flow cytometry for all clients.  

Core Technologies/Services

• Expert-operated cell sorting
• Self-service analysis
• Training for self-service analysis, and consultation

Equipment

• BD Symphony S6 (3)
• BD Influx cell sorter
• Sony MA900 cell sorter
• BD FACSAria II SORP cell sorter (2)
• BD FACSymphony A5
• BD LSR Fortessa SORP
• BD FACSCelesta

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Fisher Drug Discovery Resource Center

The Fisher Drug Discovery Resource Center (DDRC) at The Rockefeller University guides and supports researchers in drug discovery by improving the efficiency of their bioassays, identifying compounds for drug refinement and development, addressing the molecular targets for drugs, and in utilizing technologies for the measurement of drug/receptor interactions. The DDRC has a collection of 420,000 drug-like compounds, along with semi-automated liquid pipetting devices, bioassay instruments, and computational techniques for supporting drug discovery programs.

Core Technologies/Services

The DDRC provides scientific and technical support and access to instrumentation in the following areas:

• Assay Cascades used in drug discovery projects
• Miniaturized assay development
• High-throughput screening
• Identifying compounds for drug discovery or biomedical research
• Measuring the kinetics and thermodynamics of biomolecular interactions

Equipment

Automated Liquid Dispensing

• Perkin-Elmer Janus Automated Workstation
• Thermo MultiDrop Combi
• Biotek MultiFlo
• Biotek EL406 Microtiter Plate Washer with BioStack automated plate feeder

Microplate Readers and Analytical Instruments

• Molecular Devices ImageXpress Micro XL
• Biotek Synergy NEO.
• LICOR Odyssey M
• SeaHorse XF96 Extracellular Flux Analyzer

Surface Plasmon Resonance (SPR)

• Biacore 8K

Microscale Thermophores

• Nano Temper MST monolith 115

Circular Dichroism

• Applied Photophysics Chriascan V-100
• Circular Dichroism Spectrometer

Dynamic Light Scattering

• Wyatt Dynapro Plate Reader

Differential Scanning Fluorimetry (Thermal Melt Analysis)

• Bio-Rad CFX 96

Isothermal Tiration Calorimetry

• Malvern ITC200

High Throughput Mass Spectrometry

• Agilent RapidFire 360 System

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Genomics Resources Core Facility

The Genomics Resources Core Facility (GRCF) was established in 2000 and provides genomics technologies and related high-throughput technologies to the basic and translational research and clinical communities, including Weill Cornell Medicine, NewYork-Presbyterian Hospital, the Hospital for Special Surgery, and external collaborators. The full-range and high quality of Next Generation Sequencing (NGS) services include experimental design, sample manipulation, instrumentation, data analysis/interpretation, and validation. We strive to provide cutting-edge, high-quality services at affordable costs to the entire research community.

Core Technologies/Services

• Consultation
• Sample collection and quality control
• Library construction (manual and robot) and sequencing
• Single-cell library preparation and sequencing
• Genomics data analysis, management and all bioinformatics support
• Support letter and writing genomics part for Principal Investigators’ grant and manuscript preparations

Equipment

• Pacbio Revio long-read Sequencer
• Illumina high throughput NovaSeq X-Plus Sequencer
• Illumina mid throughput NextSeq2000, and NextSeq500 sequencers
• Illumina low throughput MiSeq sequencer
• Covaris High-Performance Focused-ultrasonicator R230, and Diagenode Megaruptor 3
• Sage Science Pippin HT system
• Agilent 2100 Bioanalyzer, 4200 TapeStation and Femto Pulse
• Thermo Fisher Scientific NanoDrop 8000 Spectrophotometer and Qubit Fluorometer
• BioTek Synergy Neo2S Multi-Mode Reader
• Agilent NGS workstation Bravo B, Eppendorf epMotion 5075m and SPT Firefly automated liquid handling robot
• 10x Genomics Chromium Controller and Chromium X
• Life Technologies Quantstudio 6 Flex real-time PCR system

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High Performance Computing Core

The High-Performance Computing Core provides high performance scientific computing to researchers at Weill Cornell Medicine through cutting-edge computational resources, fast on-premises storage, software deployment, application hosting, consulting and much more. Our team of engineers and developers can assist researchers in all stages of your HPC projects. We will forecast system requirements, provisioning, deployment, and monitoring of software and hardware for your research projects.

Core Technologies/Services

• Development consulting and resources for software developers
• On-premises HPC (High Performance Computing)
• Provides a high-performance, on-premises data storage system with over 3.5 PB usable capacity. It consists of a DDN SFA12KX with 840 drives. It is managed by four GPFS NSD servers, connected to clients via a 56 Gbps Inifiniband fabric.
• Offers mid-tier services for large storage, which allows researchers to preserve unused files.
• Assists with moving data to cloud-based storage providers, offering inexpensive long-term archival storage.

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Human Therapeutic Organoid Core

The Weill Cornell Medicine Human Therapeutic Organoid Core (HTOC) facility serves as a central facility for human organoid technology to accelerate organoid-based scientific discovery. Organoids are mini-organs in a dish, made up of cells that self-organize and can more accurately recapitulate human biology. Human organoid technology has arisen as one of the best models to study human development and disease. The core facility will provide human pluripotent stem cell (hPSC) derived as well as primary tissue derived organoids as a fee-for-service. The central facility will overcome the technical challenges of quality control and reproducibility often encountered when using organoid technologies.

Core Technologies/Services

• hPSC culture reagent distribution at discounted prices
• Consultation on the development and establishment of organoid systems
• Hands-on training in organoid technology
• Generation, banking, and distribution of normal human gut organoids derived from biopsy or autopsy tissues
• Generation and distribution hPSC-derived pancreatic islet organoids (sc-islets)
• Human organoid QC analyses: gene expression assessed via qRT-PCR; spatial protein localization assessed via immunofluorescence and immunohistochemistry (whole mount or cryosections); sc-islet differentiation efficiency assessed via stage specific immunostaining or flow cytometry
• Custom project therapeutic organoid development

Equipment

• Leica CM3050 S Cryostat
• Applied Biosystems QuantStudio 5 Real-Time PCR System
• Lonza 4D Nucleofector
• NL5 swept field confocal microscope
• RCM2 point scanning confocal microscope
• Cytospin 4 Cytocentrifuge
• EVOS M7000 Imaging System

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Institutional Biorepository Core

The Institutional Biorepository Core (IBC) was launched in 2017 to provide Weill Cornell Medicine investigators with a mechanism to attain high-quality human biospecimens for their research needs. The IBC is a centralized shared resource that ensures standardized research biospecimen collections with services that include solid tissue and biofluid collections, processing, and storage. The mission of the IBC is to facilitate translational research through fit-for-purpose biospecimen utilization. 

Core Technologies/Services

• The IBC serves the WCM research community, external investigators, and larger consortium projects, i.e., Lymphoma Epidemiology Outcomes/Mayo Clinic, and most recently as the East Coast biorepository site for the NIH PRISM study.
• The IBC is situated within multiple locations throughout the WCM campus and operates out of three laboratories, one of which is BSL-2 enhanced and specifically outfitted to accommodate COVID-19 processing.
• Multiple cold storage spaces containing fifteen -80 and three auto-fill LN2 freezers; they are all integrated with/supported by a cloud-based temperature monitoring system and secured by an emergency power system.
• The IBC uses OpenSpecimen to accession (intake, annotate, deidentify, barcode/label) their samples.
• It is 21 CFR Part 11-compliant and integrated with our EMR, as well as multiple research databases, i.e. REDCap, i2b2, etc.

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Metabolic Phenotyping Center

The Metabolic Phenotyping Center (MPC) offers an extensive range of services for comprehensive metabolic phenotyping in the mouse. Our extensive variety of state-of-the-art metabolic research equipment coupled with technical expertise allows the MPC to comprehensively assess murine metabolism. We work with Weill Cornell Medicine investigators to custom design investigations of dietary or microbiome manipulation, experimental drug treatment, or genetic mutation to help them answer their experimental questions.

Core Technologies/Services

• Environmental Housing
• Body Composition
• Bomb Calorimetry
• Infrared Thermography
• Glucose Metabolism
• Seahorse Analyzer XFe96

Equipment

• Promethion Metabolic Cages
• Precise Ambient Temperature and Light Control Housing
• EchoMRI
• FLIR T430sc Infrared Camera
• Agilent Seahorse XFe96 Analyzer and XFe24

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Microbiome Core

The Microbiome Core specializes in bacterial analysis and provides institutional sample-to-data processing services, and accepts a wide variety of sample types (mouse/rat
feces, human feces, human/animal swabs, pelleted cells, or just extracted DNA). With a streamlined and highly efficient process, the Microbiome Core can deliver data to customers anywhere in the world in as little as three weeks. Clients have ranged from local investigators from Weill Cornell Medicine, Memorial Sloan Kettering, and The Rockefeller University, to external users from academic institutions and commercial enterprises.

Core Technologies/Services

• 16S Sequencing: DNA extractions are performed utilizing the Promega MaxPrep & Maxwell RSC 48 system. In tandem, they provide quick DNA isolation of up to 96 samples per-day with minimal hands-on effort.
• Shotgun Metagenomic Sequencing: Like 16S processing, the Core performs DNA extractions utilizing the Promega MaxPrep & Maxwell RSC 48 system.

Equipment

• Promega MaxPrep
• Promega Maxwell RSC 48
• Promega Glomax Discover
• Perkin Elmer Zephyr G3 NGS Workstation
• Perkin Elmer GX Touch HT Nucleic Acid Analyzer
• Perkin Elmer Zephyr G3 NGS Workstation
• MiSeq (16S Sequencing; paired-end 250, 7pM loading concentration, 15% PhiX spike-in)
• HiSeq-X/NextSeq500/NovaSeq6000 (Shotgun Metagenomic Sequencing; 10pM loading concentration, 0%PhiX spike-in

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Microscopy and Image Analysis Core

The Microscopy and Image Analysis Core is comprised of three labs: Optical Microscopy, Automated Microscopy, and Electron Microscopy and Histology. The labs were established in 1998 and provide extensive training on the independent use of microscopes to Weill Cornell Medicine research faculty and staff, postdoctoral fellows, and graduate and medical students.

Core Technologies/Services

• Training on all microscopes, equipment, and image analysis and assisted microscopy sessions
• Consultation on experimental design, image analysis, and sample prep
• Sample prep and sectioning for electron microscopy and histology
• Imaging for electron microscopy and H&E staining for histology (paraffin and frozen sections)

Equipment

• Zeiss AxioScan 7 Whole slide scanner with brightfield and fluorescence imaging
• Zeiss AxioObserver 7 Widefield/fluorescence microscope
• Sartorius Incucyte SX5 HD incubator microscopy for live cell imaging
• Leica UC7 Ultramicrotome
• Aquifer HIVE Core + Data Management
• Zeiss LSM880 laser scanning confocal microscope with 7 laser lines, 2 PMTs and 1 GaAsP (32 channel spectral) detector, Airyscan and Fast Airyscan high resolution detector, incubation chamber for live cell imaging (inverted stand)
• Leica SP8 laser scanning confocal microscope (upright stand) with 4 laser lines, 1 PMT + 3 HyD detectors and a MaiTai Deep See pulsed laser and 3 HyD external detectors for Multiphoton imaging
• Zeiss Axioscope 5 wide field/histology microscope, computer & monitor
• Miltenyi Ultrascope II laser light sheet with 5 laser lines
• Separate workstations for image analysis including Imaris, ZEN, MetaMorph and FIJI
• ImageXpress Micro Confocal Imager provides automated imaging of fixed or live cells in wide field or spinning disk confocal modes with 5 fluorescence channels, transmitted light and phase contrast imaging
• 1Thermo Scientific Orbitor RS2 Microplate Mover
• Agilent/BioTek 405 TS Plate Washer
• MultiDrop384 dispensers and BioTek plate washer for sample prep
• Workstations for 2D and 3D image analysis
• JEOL JSM1400 tranmission electron microscope
• 2 Leica Ultracut T ultramicrotomes (for resin blocks)
• Pelco EasiGlow plasma cleaner
• EMS vacuum evaporator for carbon deposition on grids
• 2 Leica rotary microtomes (for paraffin blocks)
• 2 TissueTek VIP150 tissue processors (paraffin)
• 1 TissueTek paraffin embedding station with cooling plate
• Bright OTF6000 Cryostat

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Molecular Biophysics Core

The Molecular Biophysics Core was established July 2023 as a central resource hub for essential biophysics and biochemistry equipment. Originally designed to serve these sectors, the core has now expanded its services to benefit the entire WCM community. The mission is to provide seamless instrument access, user training, instrument maintenance, and promote knowledge sharing across disciplines.

Equipment

• Refeyn Mass Photometer: Refeyn TwoMP
• TA Instruments Isothermal Titration Low-Volume (Nano ITC), Standard-Volume and Automated (Affinity)
• SX-20 Stopped-Flow spectrofluorometers, single- and sequential mixing
• Zeiss AxioPlan wid field, brightfield microscope with Zeiss MrC color CCD camera
• AKTA Pure FPLC and Fluorescence detection coupled UFLC
• Anton Paar LiteSizer500 Dynamic light scattering and zeta potential measurements
• Circular Dichroism Spectrometer
• MultiDrop384 dispensers and BioTek plate washer for sample prep
• Microscale Thermophoresis NanoTemperTech Monolith NT.115
• Nanion SURFE2R

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Neuroanatomy Electron Microscopy Core

The Neuroanatomy Electron Microscopy Core provides training and services in experiments on brain tissue. These primarily include histology, pre-embedding light, electron microscopic immunocytochemical methods, and in situ hybridization techniques. The core also assists with the planning of anatomical experiments as well as data collection, analysis, and interpretation.

Core Technologies/Services

• Training in neuroanatomical methods
• Perfusion fixation of rodent brain
• Light microscopic immunocytochemistry in brain sections
• Single and dual labeling electron microscopy (EM) immunocytochemistry in brain sections
• In situ hybridization on brain sections
• General brain histology
• Quantitative analysis of light and EM specimens

Equipment

• Hitachi HT7800 transmission electron microscope
• Tecnai Biotwin transmission electron microscope
• 2 Leica Ultracut Ultramicrotomes
• 3 Leica vibratomes
• AO Sliding micotome
• HybEZ hybridization oven
• Nikon light microscopes and digital cameras

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Proteomics and Metabolomics Core Facility

The Weill Cornell Medicine Proteomics and Metabolomics Core Facility was established in 2016 and provides mass spectrometry-based analysis of proteins, peptides, metabolites, and other biochemical molecules to WCM users, as well as external users from outside academic institutions and commercial enterprises.

Core Technologies/Services

• Protein Identification
• Protein Quantitation
• Post-Translational Modification (PTM)
• Metabolomics
• Advanced and Custom Proteomics, including PTM analysis, quantitative protein interactions via AP-MS and/or proximity labeling, multiplexed protein abundance profiling
• Targeted quantitative LC-MS analysis of small molecules and peptides, including low- and high-throughput applications
• Custom proteomic method development and refinement
• Quantitative proteomics and phosphoproteomics
• Protein interaction studies using AP-MS and proximity labeling (BioID, APEX2)
• Multiplexed analysis using TMT, label-free, SILAC
• Data dependent (DDA) and data independent (DIA) proteomic analysis
• PTM mapping and discovery
• High- and low-throughput targeted analysis by MRM: metabolites; peptides; small molecules
• Data analysis: SEQUEST, MaxQuant, R, Perseus, DIA-NN, SCiLS Lab, MassHunter

Equipment

• Orbitrap Fusion Lumos
• TimsTOF Pro2
• Orbitrap Q Exactive
• Easy nLC 1200 nano flow UPLC
• Nano Elute nano flow UPLC
• Vanquish UPLC
• Agilent 1260 HPLC
• Thermo Scientific Orbitrap Fusion Tribrid
• Agilent RapidFire 365 High-throughput system
• Agilent 6495 Triple Quadrupole
• Benchbot plate handler, autosampler, and SPE
• UHPLC and Data Analysis Systems
• Agilent 1290 UHPLC System
• Thermo Scientific Easy nLC 1000 UHPLC.
• Omics Computing Proteome Destroyer PC