NJMS Research Core Facilities

ADVANCING RESEARCH THROUGH INNOVATION Explore the new cutting-edge scientific technologies in our shared research facilities at Rutgers New Jersey Medical School, where innovations drive groundbreaking scientific discoveries and medical progress.

njms.rutgers.edu/research

At Rutgers New Jersey Medical School (NJMS), we are dedicated to advancing medical research and training the next generation of scientists. Our core research facilities serve as an integral part of this mission, providing the tools and resources needed to drive medical breakthroughs that can have a global impact.

Learn more about the NJMS Office of Research. njms.rutgers.edu/research

NJMS Research The core research facilities at NJMS are at the forefront of scientific discovery, equipped with cutting-edge technology, and home to internationally renowned researchers. This resource plays a vital role in advancing medical knowledge and fostering innovation in key research areas such as neuroscience, cancer research, and infectious diseases. The facilities are led by world-class researchers and external partners, driving breakthroughs that improve patient care and public health.

The Office of Research provides: A collaborative research environment that encourages cross-disciplinary innovation.

Core Facilities Flow Cytometry & Immunology Core Laboratory Cryo-Electron Microscopy Core Facility Cellular Imaging & Histology Core Genomics Research Core Regional Biocontainment Laboratory Advanced Preclinical Imaging Lab

High-quality equipment and cuttingedge technology to support your research endeavors.

Opportunities to work alongside worldrenowned researchers who are making groundbreaking discoveries.

Center for Advanced Metabolomics and Proteomics and Metabolomics Research (CAMPR) Gnotobiotic Core, joint with Rutgers Animal Care Services Molecular and Genomic Informatics Core (MaGIC)

Explore the New Technologies in Our Core Facilities Flow Cytometry & Immunology Core Laboratory Scientific Director: Patricia Fitzgerald-Bocarsly, PhD; bocarsly@njms.rutgers.edu Technical Director: Sukhwinder Singh, PhD; singhs1@njms.rutgers.edu Scan the QR code to view the lab’s website. njms.rutgers.edu/fcic

BD FACSymphony™ S6 System Housed in the Regional Biocontainment Laboratory (see below)

BD FACS Symphony A5 SE The BD FACS Symphony A5 SE is a high-performance flow cytometer analyzer for single-cell multiparameter analysis, equipped with a full-spectrum detection of light emissions by fluorescent probes. This technology allows researchers to detect up to 48 different biomarkers parameters.

Intellifex-RUO xMAP The Intellifex-RUO xMAP is a high-throughput multiplex platform designed for simultaneous analysis of up to 48 biomarkers using advanced Luminex® technology.

This system excels at measuring key immune factors such as cytokines, chemokines, and growth factors, and supports immune assays, including ELISA and ELISpot, and suitable for analyzing serum, plasma, and cell culture samples.

Cryo-Electron Microscopy Core Facility

Scientific Director: Vasileios Petrou, PhD; vasileios.petrou@rutgers.edu Technical Director: Alex Wei, PhD; h.wei@rutgers.edu

Thermo Fisher Tundra Next-Generation Cryo-TEM

The Tundra Next-Generation Cryo-TEM is a cutting-edge tool for microscopic imaging of proteins and macromolecules. Featuring a 100kV Transmission Electron Microscope with autogrid capability, it offers high-resolution 2D and 3D imaging at an entry-level. Support instruments include the Thermo Fisher Vitrobot Plunge-Freezer for rapid sample vitrification ensuring high-quality cryo-fixation results and a high sample preparation throughput prior to cryo-TEM observation and the Agar Scientific Easiglow Glow Discharge System to support sample grid preparation.

Thermo Fisher Vitrobot Plunge-Freezer

Agar Scientific Easiglow Glow Discharge System

Cellular Imaging & Histology Core

Scientific Director: Dongfang Liu, PhD; dongfang.liu@rutgers.edu Technical Director: Luke Fritzky; fritzklf@njms.rutgers.edu

Scan the QR code to view the lab’s website. njms.rutgers.edu/cihc

Akoya Phenocycler-Fusion 2.0 The Akoya Phenocycler-Fusion 2.0 offers spatial microscopic imaging with precise multiparameter detection of proteins within tissue samples. This system can detect more than 60 different protein biomarkers in a single tissue section. Funded by an NIH S10 Grant, PI Jason Weinstein, PhD.

Images courtesy of Akoya

Zeiss Axioscan 7 Slide Scanner The Zeiss Axioscan 7 is a rapid, high-resolution slide scanner designed for the microscopic whole slide imaging of standard brightfield illuminated histology slides as well as slides labeled with multiple fluorescent dyes. The digitized slides can be viewed and analyzed using standard computer systems.

Cellular Imaging & Histology Core

Scientific Director: Dongfang Liu, PhD; dongfang.liu@rutgers.edu Technical Director: Luke Fritzky; fritzklf@njms.rutgers.edu

Leica Stellaris 8 tau-STED Confocal Microscope The Leica Stellaris 8 tau-STED is a fully tunable spectral laser scanning confocal microscope. The instrument features Leica’s White Light Laser enabling excitation of fluorochromes from 440 nm ton 790 nm and includes a tunable spectrophotometer-based detector. The system is also equipped with two STED depletion lasers enabling Super-Resolution imaging with axial resolutions below 50 nm.

Instruments Imaris Imaging Software Imaris is a sate-of-art 3D/4D visualization and analysis software platform for advanced multidimensional microscopy images. Imairs for Core Facilities includes packages for automated object detection, filament tracing, 4D tracking, AI powered object classification, GPU accelerated deconvolution and large format tile stitching. The Cellular Imaging and Histology Core maintains a high-end Xenon workstation dedicated to running Imaris.

Organ: Lung

Confocal micrograph Images courtesy of Wiesner Lab

Spatial Transcriptomics

In collaboration with with the Molecular and Genomic Informatics Core (MaGIC)

The 10x Genomics Xenium instrument is an imaging based in situ spatial biology platform providing subcellular expression profiling of hundreds to thousands of genes in a single tissue section. 10x Genomics offers both predesigned off-the-shelf panels as well as custom designed panels for use in the Xenium Analyzer. The 10x Genomics VisiumHD is a sequencing based spatial gene expression platform enabling the unbiased analysis of the whole transcriptome in a single tissue section. The 10x Genomics CytAssist ensures the accurate transfer of probes from a tissue section to the capture area on a VisiumHD Slide. The resulting spatially encoded cDNA library is then sequenced on an Illumina Next Gen Sequencer and gene expression data is then mapped back to a scan of the original tissue section preserving spatial context.

Xenium In Situ Cellular Spatial Imaging ®

Visium HD Human and mouse gene expression localized within bio specimen tissue architecture

Spatial Transcriptomics

In collaboration with with the Molecular and Genomic Informatics Core (MaGIC)

Xenium In Situ Single Cell Spatial Imaging Image courtesy of 10x Genomics, Inc.

Visium HD Human and mouse gene expression ®

Image courtesy of 10x Genomics, Inc.

Genomics Research Core

Director: Milind Mahajan, PhD; mm3711@njms.rutgers.edu

Scan the QR code to view the lab’s website. njms.rutgers.edu/genomics

New Next Generation Sequencing platform: Illumina NovaSeq X plus

The Illumina NovaSeq X Plus is an upgraded highthroughput deep genome sequencing platform designed for faster and more cost-effective sequencing.

The new XLEAP-SBS chemistry delivers increased accuracy and instrument performance. With a higher throughput volume, it offers single-cell sequencing at half the cost. This system is capable of up to 52 billion single reads and 104 billion paired-end reads with onboard cluster generation, and accelerated data analysis using an onboard DRAGEN platform.

Nanopore GridION Sequencing System

The Nanopore GridION is a long-read next-generation sequencing system that supports multiple platforms running together, offering microbiome strain identification and clinical biomarker-filling analysis, filling in sequencing gaps, and providing improved statistical power.

Agilent BioTek Cytation 7 Cell Imaging Multi-Mode Reader

The Agilen BioTek Cytation 7 is a versatile, highthroughput multimodal microplate reader with advanced imaging capabilities. It supports automated digital upright and inverted widefield microscopy for fluorescence and brightfield detection with a widerand more sensitive range of fluorophore detection.

**New Spatial Transcriptomics Technology Joint with Cellular Imaging & Histology Core** Illumina 10x Genomics Visium hd/CytAssist Xenium technologies

Regional Biocontainment Laboratory (RBL) RBL Director: David Alland, MD; allandda@njms.rutgers.edu Animal models and related services (AMRS) core Core Director: Padmini Salgame, PhD; salgampa@njms.rutgers.edu Co-Directors: Ricardo Rajsbaum, PhD; ricardo.rajsbaum@rutgers.edu John Chan, MD; jc2864@njms.rutgers.edu Technical Director: Preeti Bharaj, PhD; pb607@njms.rutgers.edu

Scan the QR code to view the lab’s website. njms.rutgers.edu/rbl

Equipment for Monitoring Respiratory Functions in Infectious Disease Research Funded by an NIH UC7 Grant, PI Dr. David Alland, MD.

Sireq flexiVent® Complete System Solution (FV-FXCS) An advanced system for monitoring and measuring in vivo respiratory functions. It goes beyond traditional resistance and compliance mechanics of pulmonary ventilation, and captures crucial details about the mechanical properties of conducting airways, terminal airways and parenchyma

Regional Biocontainment Laboratory (RBL) RBL Director: David Alland, MD; allandda@njms.rutgers.edu Animal models and related services (AMRS) core Core Director: Padmini Salgame, PhD; salgampa@njms.rutgers.edu Co-Directors: Ricardo Rajsbaum, PhD; ricardo.rajsbaum@rutgers.edu John Chan, MD; jc2864@njms.rutgers.edu Technical Director: Preeti Bharaj, PhD; pb607@njms.rutgers.edu

BD FACSymphony™ S6 System The BD FACSSymphony S6 offers single-cell, multi-color flow cytometry analysis and cell sorting, with the ability to simultaneously collect up to 6 distinct cell subpopulations.

This system features full-spectrum detection of light emissions from fluorescent probes, identifying up to 50 biomarker parameters.

Molecubes X-CUBE MicroCT Imager A high-throughput benchtop micro-CT scanner designed for preclinical imaging analysis. This scanner will be part of an respiratory infectious disease animal modeling lab in the RBL, supporting studies of bacterial and viral transmission and chronic infection.

Advanced Preclinical Imaging Lab

Technical Director: Sushil Tripathi, PhD; st1123@research.rutgers.edu

MiLab VECTor6 PET/SPECT/CT The MiLab VECTor6 is a multi-modal live imaging system for small animal studies. This system includes PET, microCT, and SPECT imaging capabilities. Applications include regional glucose uptake in tumors/brains; lung injury; bone mineral density and studies monitoring biomaterials and devices.

Funded by an NIH S10 Grant, PI Roger Howell, PhD. Scientific Director: Roger Howell, PhD.

Advanced Preclinical Imaging Lab

Technical Director: Sushil Tripathi, PhD; st1123@research.rutgers.edu

Revvity (formerly Perkin Elmer) IVIS Spectrum II An in vivo animal imaging platform for non-invasive monitoring of disease progression through bioluminescence and fluorescence detection. It offers high sensitivity in deep tissue and can simultaneously image up to 5 mice. The rotating camera enables 3D capabilities, while the software allows co-registration with MiLabs PET, SPECT, and microCT. Funded by an NIH S10 Grant, PI: Punima Bhanot, PhD.

Center for Advanced Metabolomics and Proteomics Research (CAMPR) Director: Hong Li, PhD; liho2@njms.rutgers.edu

Scan the QR code to view the lab’s website. njms.rutgers.edu/capr

Spatial Metabolomics: Waters DESI-Synapt This instrument combines mass spectrometry with microscopic detection of metabolites allowing for spatial mapping of molecular events of metabolism within tissue architecture. Scientific Director: Tania Wong, PhD.

**New Mass Spectrophotometer Now Operational** NIH S10 Awarded Bruker timsTOF Ultra 2 LC-MS System for high performance proteomics, PI Hong Li, PhD

Shared Equipment

Lonza Nucleofector® Technology A cutting-edge platform for efficient transfection of even non-dividing primary cells, such as resting T cells or neurons, with rapid gene expression and modification. Key applications include the CrisprCas9 technology for site directed mutations, as well as gene expression and deletions.

Physiological Metabolic Monitoring: Sables System Promethion Core® For in vivo metabolic and behavioral phenotyping. This system provides highresolution, physiological metabolic and behavioral phenotyping in a 22-cage housing setup. It is equipped with a triple gas analyzer (O₂, CO₂, H₂O), 3D infrared beam detection, body weight monitoring, a running wheel module, and an environmental sensor array for recording ambient temperature, light, RH, sound, BP, noise, and motion data.

Scientific Director: Tania Wong, PhD.

Echo 650 Acoustic Liquid Handler This instrument is a high throughput, accurate, precise, and contact-free acoustic transfer system to dispense sample volumes as low as 2.5 nL. Transfers from 96-well to 1536-well microplates are supported, enabling assay miniaturization in a broad range of applications.

Funded by an NIH S10 grant, PI David Alland, MD, Public Health Research Institute Center.