Atomic Force Microscopy Core Facility

Center for Advanced Genomics Technology (CAGT)

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
  • %