Departmental Cores & Facilities

Microscopy

Cancer Registry

GCF Website

What

The Genomics Core Facility at the Icahn School of Medicine at Mount Sinai currently operates a diverse world-class next generation sequencing platform (NGS) suite directed by Robert Sebra, Ph.D. alongside Associate Director, Kristin Beaumont, Ph.D. (single cell molecular biology & sequencing), and Assistant Director, Mike Beaumont, Ph.D (physiology and functional validation) who guide sequencing/molecular and single cell technologies. Since 2013, the team has successfully published 120 collaborative high-impact publications and has played an ample role in submitting dozens of grants which have been funded across various disease foci including cancer, inherited disease, structural variation, infectious disease and innovative technology development.

Fees

Fees vary by project.

Office Location

14th Floor – 14-20E
1425 Madison Ave
New York, NY 10029

Main Laboratory

13th Floor, Room 13-02
Sequencing Instrument Room
14th Floor, Room 14-59

Contacts

Robert P. Sebra, PhD
Professor, Genetics and Genomic Sciences
Director, Center for Advanced Genomics Technology
Director, Genomics Technology Facility 
Icahn Genomics Institute 
Black Family Stem Cell Institute
Icahn School of Medicine at Mount Sinai
1425 Madison Ave, New York, NY 10029

Kristin Beaumont, PhD
Assistant Professor, Genetics and Genomics Sciences
kristin.beaumont@mssm.edu

Equipment List

The Genomics Technology Facility

The Genomics Technology Facility occupies >4500 square feet and is located on the 13th and 14th floor of the 1425 Madison Ave., Icahn Building at the Icahn School of Medicine at Mount Sinai main campus. The GTF’s main wet lab space is housed as part of the Center for Advanced Genomics Technology (CAGT) on the 13th floor and spans molecular, single cell, and tissue culture spaces, and sequencing and technical facilities are located on the 14th floor. The space assigned to the GTF consists of 12 office or desk spaces, ~20 laboratory benches and standalone tissue culture, and single cell and spatial transcriptomics lab spaces. Three biosafety cabinets for tissue culture available for the lab, alongside the molecular and dry lab benches to allow for dynamic interactions between students and facility faculty, and lab staff. Additional laboratory storage equipment includes over 6 -80C freezers, 6 -20C freezers, multiple +4C fridges, 2 incubators, numerous centrifuges, as well as size selection and various quality control equipment. The GTF lab is also responsible for 2 MiSeq, 2 NovaSeq, 2 NextSeq550, 2 Illumina MiniSeqs,1 PacBio Sequel instrument, 3 PacBio Sequel II instruments, 3 Ion S5XL instruments, 1 Genexus Integrated Sequencer, 1 Nanostring nCounter, 5 10X Genomics Chromium instruments, 1 Oxford Nanopore GridIon configuration, 3 Ion Chefs from Ion Torrent/Thermo-Fisher, 1 Berkeley Lights Beacon system, 5 Chromium 10X Genomics instrument, 1 Chromium X instrument, 1 Nanostring GeoMx, 2 MissionBio Tapestri system and one CelSee Genesis platform.

Expanded Technology Development Facility

Next Generation Sequencing Equipment 

• Two Illumina NovaSeq – The highest throughout sequencer available from ILMN and most flexible for arranging modular sequencing pipelines for generating extremely large data sets.
• Two Illumina NextSeq 550 – Similar to ILMN 2500 but with rapid data generation capability and extremely useful for single cell sequencing purposes.
• Two Illumina MiSeq: A primary instrument for targeted panel sequencing and sequencing of small genomes using Illumina chemistry.
• Two Illumina MiniSeq:  An instrument for targeted and rapid panel sequencing of small genomes or amplicon panels with speed beyond MiSeq capability and also useful for QC methods.
• One Pacific Biosciences Sequel systems – Continuous long read sequencing at ~7X the capacity of standard RSII systems
• Three Pacific Biosciences Sequel II systems – Continuous long read sequencing with ~56X capacity of the RSII platforms.
• Three Ion S5XL instruments: Second generation high through put rapid run sequencers from Torrent, particularly suited for targeted diagnostic sequencing assays.
• One Ion Torrent Genexus Integrated Sequencer:  Low throughput automated rapid run sequencer from Life Technologies, particularly useful for low gene number or hotspot targeted sequencing purposes.
• Three Ion Chefs:  Used for automation of library enrichment and sequencing chip preparation for the Ion S5 System.
• One Nanostring nCounter system: Amplification-free RNA analysis, simplified gene expression analysis by counting molecules directly
• Five 10X Genomics Chromium and one Chromium X systems for constructed linked long reads using UMI and droplet technology toward structural variation discovery in WES and WGS data.
• One Illumina HiScan: Provides best possible gridding and scanning of new generation Illumina Bead Arrays used for Genome Wide Association Studies (GWAS), Pharmacogenomics, Methylation, gene expression, Goldengate, and custom genotyping analyses.
• One Illumina Bead Express System:  For veracode genotyping assays.
• One Applied Biosystems 7900HT – Real-Time thermocycler with robotic loader for quantitative PCR and end-point allele discrimination.
• GridIon Oxford Nanopore Sequencing capability
• Advanced Analytical FEMTO Pulse Automated Pulsed-Field CE instrument – Allows for the rapid automated detection, quantification and quality assessment of low concentration DNA and RNA samples (down to 5 fg/uL) and very large fragments (up to 200 kb)

Assays available – short read bulk sequencing 

• RNA Bulk sequencing library preparation:
  • Illumina Stranded Total RNA with RiboZero Plus
  • Illumina Stranded mRNA
  • SMART-Seq v4 Ultra Low Input
• DNA Bulk sequencing library preparation:
  • Illumina DNA Prep (Previous Nextera Flex WGS)
• smRNA:
  • SMARTer smRNA-Seq Kit for Illumina
• ATAC
  • Active Motif ATAC-Seq Kit
• Immune Profiling:
  • NEBNext Immune Sequencing Kit
• Various custom Assay by consultation
• User-prepared libraries for NGS sequencing
• Ion Torrent:
  • Oncomine v3 (targeted DNA or DNA + RNA)
  • Ampliseq (commercial or custom DNA/RNA panels)
  • Ampliseq HD (commercial or custom DNA/RNA liquid biopsy or low input panels)
  • ReproSeq (1-10 cell aneuploidy panel)
• nCounter:
  • Commercial or Custom assays

Assays available – long read bulk sequencing 

• Continuous Long Read (CLR) whole genome sequencing
• HiFi whole genome sequencing
• Low input/ultralow input whole genome sequencing
• Isoform sequencing (IsoSeq)
• Targeted IsoSeq
• Amplicon sequencing
• HLA genotyping

Single Cell & Spatial Transcriptomics Equipment 

• One Berkeley Lights Beacon: For isolation of up to 1000 single cells (or batches of cells) for single cell or low input real-time cellular biology and isolation purposes in combination with various molecular pipelines for the amplification of selected single cells.
• Five 10X Genomics Chromium and one Chromium X system for high throughput 3’ RNA Sequencing of thousands to tens of thousands of single cells for subclonal identification and expression analyses. We are also a CSP provider for Visium spatial transcriptomics.  Aside from that, we offer all immune profiling, CITESeq, ATACSeq, and additional development based single cell assays using these instruments.
• One CellSee single cell Platform: for medium to high throughput cell selection and custom methods development applications.
• One MissionBio Tapestri platform: for commercial and custom targeted amplicon DNA and protein sequencing at the single cell level.
• One Nanotring GeoMx 2D spatial transcriptomics instrument to enable 2D spatial profiling of selection ROIs to determine transcriptional DGEA capabilities with targeted transcriptomics on FFPE and other tissue formats.
• One Veranome in-situ SPLIT-FISH spatial profiling instrument for sub-cellular resolved spatial transciptomics 

Assays Available (all are custom designed and require consultation)

• 10x Chromium single cell RNA Seq or single cell RNA Seq + cell surface protein expression (3’ or 5’ gene expression + TotalSeq B)
• 10x Chromium single nuclei RNA Seq (3’ or 5’ gene expression)
• 10x Chromium single cell ATAC Seq
• 10x Chromium single cell RNA Seq + VDJ immune profiling (5’ gene expression only)
• 10x Chromium multiome single nuclei RNA Seq + ATAC Seq
• Mission Bio Tapestri DNA or DNA + Protein (commercial or custom panels + TotalSeq D oncology cocktail)
• 10x Visium or 10x Visium FFPE spatial transcriptomic profiling
• Nanostring GeoMx commercial or custom assays
• Various early access programs for in-situ, spatial transcriptomic profiling

Sample preparation and storage Equipment 

• One Agilent Bravo: Automated robotic system for library creation for next generation sequencing (available via the Genomics Core Facility, GCF).
• Two Tecan Evos: Automated robotics systems for sample preparation for Illumina HiScan (available via the GCF).
• One Covaris E210: Focused Acoustic Disrupter/Sonicator for automated high yield preparation of multiple genomic/mRNA libraries (available via the GCF).
• One Tape Station and three Agilent BioAnalyzer 2100s: Microfluidics-based platform for sizing, quantification and quality control of DNA and RNA; crucial in preparation of libraries for all sequencing platforms.
• One Sage Blue Pippin: Size-selection purification instrument for generating long fragment libraries for long read (Pacific Biosciences or Oxford Nanopore) sequencing and genome finishing purposes.
• One Sage Blue Pippin HT: Size selection instrument that has ~3X the capacity of a Blue Pippin instrument
• One Sage Pippin ELF: Allows for high throughput size selection of multiple bands within a single sample, as opposed to a single targeted band as utilized in the Blue Pippin series.
• One Sage HLS: Size selection instrument that accepts cells as input for HMW DNA isolation
• One Beckman Biomek FX: Automated robotics system for accurate liquid handling tasks, including real time PCR set up in 384 wells, as well as automated sequencing reaction cleanup and DNA quantity normalization for high throughput genotyping on microarray (available via GCF).
• 12+ Thermocyclers
• Various sample storage formats at -80C, -20C, and 4C.

Assays Available

Sample quality control  

• qPCR – 96 or 384 well plates
• Qubit
• Bioanalyzer
• Tapestation
• Covaris Shearing
• Speedvac concentrator

Genomics Microarray

CRU Website

What

The Clinical Research Unit (CRU) provides infrastructure to perform clinical and translational research studies including:

• Outpatient Space
• Nursing Support
• Specimen Processing
• Walk-in Phlebotomy
• Pre-procedure COVID testing (for research studies only)

For more information refer to CRU Resources and watch the CRU Video Tour.

Equipment List and Photos

For a list of CRU equipment and photos, see the CRC Vault.

Fees

Refer to the CRU Fee Schedule.

Hours

8:00 AM – 5:30 PM (Monday – Friday, except hospital holidays)

Walk In Phlebotomy Services – 9:00 AM – 4:30 PM (Monday-Friday, except hospital )

How

Investigators interested in using CRU services must complete an application and receive approval from the CRU Administration Committee. Requests to use the CRU services may be assigned through the IRB/RUTH submission process by completing the Ancillary Review Form and assigning CRU via the Manage Ancillary Review tab. Applications should be completed in its entirety (budget page included). Investigators will receive notification of approval via email communication with the CRU and/or through RUTH.

When

Applications can be included with the IRB/RUTH submission. To avoid delays, investigators are encouraged to speak with the CRU, CRU@mssm.edu prior to submitting applications.

In-service

An in-service meeting with the CRU team may be required prior to scheduling services. At the in-service, the study protocol and procedures will be discussed to ensure that all of the elements are in place to safely and effectively begin the study. For more information refer to the web page – Clinical Research Unit (CRU).

Clinical Research

The COVID Clinical Trials Unit (CTU), under the Division of Infectious Diseases, was established after the 1st wave of the pandemic to orchestrate the many ongoing COVID-19 clinical investigations throughout the Mount Sinai Health System (MSHS).

Since its inception, the COVID CTU has participated in several landmark COVID-19 studies, including the evaluations of the Regeneron monoclonal antibodies as well as the Pfizer and J&J vaccines. The COVID CTU continues to enroll research volunteers in both inpatient and outpatient settings.

To avoid overlapping efforts, all COVID-19-related clinical trials at MSHS, after receiving approval from the COVID-19 Protocol Review Committee, should then coordinate the study through the COVID CTU. All COVID-19 related protocols must be submitted to the COVID CTU for review and implementation. The COVID CTU will work directly with investigators to submit budgets, contracts, and other regulatory needs. Furthermore, the COVID CTU can provide research staffing support at most MSHS hospitals if additional staffing is needed.

For further information, please contact Debbie Lucy, COVID CTU Program Manager, at 212-824-7714 or email debbie.lucy@mssm.edu.

Histology and Pathology

The Mount Sinai Department of Health Education partners with our health system colleagues and our community to promote access to and engagement with the information, services, and resources individuals and families need to live their healthiest lives. We believe that everyone deserves access to affirming, inclusive, and appropriate health information that is actionable and empowering and reflective of the diverse communities we serve. Our goal is that our community members understand the Mount Sinai Health System to be a reliable, trustworthy, and committed partner in addressing health disparities and supporting community health. We are driven by our commitments to advancing racial justice and health equity on the systemic, institutional, and individuals levels.

Our scope of services include:

• Internal consultation on patient-facing health education content creation, and the development of provider-facing tools and resources
• Professional development for staff on topics such as health literacy, risk communication, motivational interviewing, and creating health literate print resources
• Health education program development and implementation
• Health system consultation and partnership on equity- and education-related initiatives

 
Health Education

CTO Website

The Clinical Trials Office (CTO) provides infrastructure to support investigators within the Department of Medicine conduct industry sponsored clinical trials.

Resources

• Protocol Feasibility Assessments
• Support with Department of Medicine Protocol Review Committee (PRC) Submission
• Regulatory Submission and Management
• Financial Management
• Study Coordinator Support
• Recruitment Support

Departmental Cores Website

Departmental Cores Website

The Molecular Modeling Core specializes in supporting research on macromolecular structures in silico studies of proteins and nucleic acids. Such studies can include:

Visualization

• Ab initio structure prediction of small molecules (either using quantum mechanics or molecular mechanics)
• Homology modeling of proteins
• Virtual screening (docking)
• Computer simulations (molecular dynamics or Monte Carlo)

The Core offers help in:

• Installing and using visualization software (e.g., Pymol or VMD)
• Structure prediction and manipulation software (e.g., Marvin, Avogadro)
• Using software installed on our supercomputer, Minerva (e.g., Gaussian, Charmm, Amber, NAMD, and MMC; as well as several docking programs, such as Autodock-4, Autodock-Vina, and DOCK)

Students interested in molecular modeling tools can take the course “BSR2104 Intro to Computer Modeling & Macromolecules.” For assistance in using the Core, as well as tutorials and consultations, refer to the Mezei Laboratory site.

Mihaly Mezei, PhD, Director
Tel: (212) 659-5474 (x85475)
mihaly.mezei@mountsinai.org

Proteomics

Website

Mount Sinai BioDesign is a technology and device incubator as well as an engineering laboratory and prototyping facility for the Mount Sinai Health System. The group is dedicated to a needs-driven approach to innovation in medicine, inspired and advised by Mount Sinai faculty and staff to translate clinical knowledge into commercially-relevant products, often together with industrial collaborators. The group incorporates engineering, project management, and clinical resources towards its goal of empowering the Mount Sinai community to translate technological innovations and deliver them into the hands of physicians and patients. The group also supports research efforts in medical artificial intelligence with resources and mentorship through the graduate programs in Artificial Intelligence and Emerging Technologies, and in technology related clinical trials together with the Department of Population Health.

Resources

• Design & Engineering Consultations
• Manual Fabrication
• Digital Fabrication and Design
• Medical Modeling
• Prototyping
• Equipment
  • 3D Printers
  • Laser Cutter
  • Parylene Deposition System
  • CNC mill
  • Hand and Power Tools
  • Other Postprocessing Capabilities

Artificial Intelligence Biodesign Fabrication Incubators Medical Devices

Scientific Computing and Data Website

Scientific Computing and Data provides the computational and data infrastructure to accelerate scientific discovery at Mount Sinai.

Services

High-Performance Computing

• Minerva Supercomputer
• NIH STRIDES Access

Data Resources

• Data Ark: Data Commons
• HHEAR and HADatAc
• Oncology Clinical Annotation Project (CAP)
• Mount Sinai Data Warehouse
• NCATS National COVID Cohort Collaborative (N3C) Data Enclave

Data Capture Tools

• Electronic Research Application Portal (eRAP)
• REDCap

Other Services

• Digital Concierge Service
• Honest Broker Service for EMR research
  • Proficiency in database management, SQL scripting, and EHR database design
  • HIPAA trained, responsible conduct of human subject research
  • Compliant with all regulatory frameworks.

Transfusion Medicine and Cellular Therapy Website

The Transfusion Medicine and Cellular Therapy Laboratories in the Department of Pathology, Molecular and Cell-Based Medicine provide infrastructure, expertise and services to support clinical research.

Resources

• The Blood Bank
• Cellular Therapy Laboratory
• The Apheresis Center

Transfusion Medicine and Blood Bank

The Tumor CytoGenomics Laboratory in the Department of Pathology, Molecular and Cell-Based Medicine, provides expertise in cancer cytogenetic techniques and analysis. The laboratory offers a full range of services to support clinical and basic research.

Resources

• Tumor CytoGenomics Laboratory Clinical Services
• Clinical Tests
• Disease-Specific FISH Panels
• Consultation Services

CytoGenomics