Research Core Services

The Lerner Research Institute's Core Services seek to facilitate and advance research throughout Cleveland Clinic by providing technologies that support basic, translational, and clinical research.

Research Cores

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Flow Cytometry Core



The Flow Cytometry Core has acquired a new high performance, fixed alignment cuvette cell sorter that makes sorting easier and more accessible. The Stem Cell Biology and Regenerative Medicine Department courteously funded the Special Order BD FACSAria II. The new sorter improves ease of use, flexibility, and aseptic capability making it the best choice for consistent results in sorting across a broad range of applications.

A BioProtect III Walk In Clean Air and Containment Cabinet houses the FACSAria II. The BioProtect III is a specialty type Class II biological safety enclosure designed to offer personnel, product, and environmental protection from potentially aerosolized biological hazards.

The Special Order BD FACSAria II consists of 488nm, 640nm, 405nm, 561nm and 355nm lasers, providing 16 parameters. The optical filters detect the following fluorophores:

  • Blue laser - FITC, PerCP-Cy5.5
  • Red laser - APC-Cy7, Alexa 700, APC
  • Yellow-Green laser - PE, PE-Cy5, PE-Cy7, PE-TxRd, mCherry and DsRed
  • Violet laser - Pacific Blue, Qdot 585, Qdot 605, Qdot 655, AmCyan and Qdot 565
  • UV laser - DAPI, Hoechst, Indo-1, Side Population Filter Set

Additional options included:

  • 70-, 85-, 100- and 130-micron nozzle tips
  • Two- and four-way sorting into microtubes, 12 x 75-mm tubes, and 15 mL tubes
  • Accepts various sizes of sample input tube
  • Automated Cell Deposition Unit (ACDU) allows for multi-well plate and slide sorting
  • Cooling system for the sort collection device (tubes and multi-well plates)
  • Aerosol Management for enhanced removal of aerosols


Scanning is achieved by using the Becton-Dickinson LSRII flow cytometer. The instrument has highly sensitive lasers used exclusively for quantitative analysis. The LSRII is capable of 12 color and 14 parameter acquisition with 5 lasers (Argon ion 488nm, HeCd UV 355nm, Violet 405nm, HeNe 639nm, and Green 532nm).
(LSRIIConfig.pdf )

BD LSR Fortessa

The Flow Cytometry Core has recently acquired a Special Order BD LSR Fortessa cell analyzer that has the flexibility to support the expanding needs of multicolor flow cytometry assays. The BD LSR Fortessa cell analyzer offers the ultimate in choice for flow cytometry, providing power, performance, and consistency. It is designed to meet the multicolor analysis needs of complex experiments that require a specific combination of unique lasers, detectors, and filters (FortessaConfig.pdf )

Purchase of the instrument was generously made possible by a grant awarded to Dr. Aaron Fleischman (Principal Investigator) in collaboration with Dr. Roy Silverstein, Tom McIntyre, Keith McCrae, Frank Papay, Gary Procop and Rishi Singh to pursue a project entitled "Multi-User BioSensor Integrated Platform?. The goal of the studies proposed is to create a center for business and academic users that will enable research and development of micro-fluidic and nano-fluidic systems and sensors for medical applications. The project is supported by a 3-year, $2.6M equipment grant sponsored by the "Ohio Third Frontier Wright Center for Sensors Systems Engineering?. The project combines capabilities available at the Cleveland Clinic, Case Western Reserve University, Cleveland State University and Ohio businesses to develop a center for the rapid prototyping and testing these systems. Initial focus areas are drug delivery, wound healing, cellular diagnostics, and pathogen detection. Resources will also be purchased to support rapid prototyping and testing of multi-layer, micro-fluidic and nano-fluidic systems, cell and biomarker characterization, and integration of micro sensors.

Fortessa technical details:

The BD LSRFortessa SORP consists of 488nm, 640nm, 405nm, 561nm and 355nm lasers, providing 20 parameters. The optical filters detect the following fluorophores:

  • Blue laser - FITC, PerCP-Cy5.5
  • Red laser - APC-Cy7, Alexa 700, APC
  • Yellow-Green laser - PE, PE-Cy5, PE-Cy7, PE-TxRd, mCherry and DsRed
  • Violet laser - Pacific Blue, Horizon V450, Qdot 700, Qdot 605, Qdot 655, AmCyan, Horizon V500 and Qdot 585
  • UV laser - DAPI, Hoechst, Indo-1 AM

Additional options included:

  • High Throughput Sampler (HTS) Option
  • Side Population Filter Set
  • Additional Filter Set for mOrange and Tomato


The Flow Cytometry Core is now offering the use of the Countess? automated cell counter. The Countess™ provides fast, easy and accurate cell counting without using a hemocytometer, eliminating the tedium and subjectivity of manual cell counting. Automated counting frees up your time and minimizes subjective judgments that can lead to error.

The Countess™ instrument:

  • Counts live and dead cells
  • Calculates percent viability
  • Measures average cell size
  • Calculates dilutions for downstream applications
  • Uses just 10 microliters of sample
  • Saves your data to a USB drive

High Throughput Sampler (HTS)

The High Throughput Sampler (HTS) option is now available in the Flow Cytometry Core. In addition to single tubes this feature allows acquisition of samples from 96- or 384-well microtiter plates. Experiments with large number of samples are becoming increasingly common. The ability to acquire in "batch? mode can increase productivity by allowing investigators the ability to multitask during sample acquisition. The speed of acquisition in high-throughput mode is <15min per 96well plate (2 sec acquisition per sample). Sample carryover from the HTS is <1%.

Before planning an experiment which utilizes HTS acquisition, a meeting with Flow Core personnel is required.

A 15-minute set-up fee will be included for all HTS use.

Apogee A50 Micro Flow Cytometer

The Apogee A50- Micro is specifically designed for measuring sub-micron biological particles. The instrument was purchased to meet the increasing demand of LRI investigators to study microparticles. Emerging evidence shows that microparticles play critical role in a growing list of processes such as inflammation, infection, immune responses, thrombosis, cancer metastasis and angiogenesis. It’s only a matter of time before new microparticle-based diagnostic and prognostic tests will be developed and become part of standard clinical care, a progress that was previously hampered by technical challenges of how to enumerate and characterize these microvesicles.
The Apogee A50- Micro provides accurate analysis and fluorescence measurements of:

  • microparticles
  • virus particles
  • bacteria
  • yeast
  • exosomes
  • nanoparticles
  • platelets

With a detection limit of <100nm and <10nm resolution, a technical ingenuity lacking in standard flow cytometers, the Apogee Micro Flow Cytometer is designed for analysis of microparticles. We are currently one the very few institutes in the USA who offers this service.
Apogee technical details:
Our Apogee A50 Micro consists of a 488nm laser, providing 6 parameters. The optical filters detect the following most commonly used fluorophores: (ApogeeConfig.pdf)

  • Green Fluorescence - FITC, Calcein, CFSE, A488, EGFP
  • Orange Fluorescence - PE, PE-Cy5
  • Red Fluorescence - PerCP, PerCP-Cy5.5, PerCP-ef710
  • Deep Red Fluorescence - PE-Cy7

Fluidigm C1 Single-Cell Auto Prep System

The C1 Single-Cell Auto Prep System offers a fully automated and streamlined workflow to capture single cells and process each cell individually for sequencing and gene expression analysis. This single-cell precision technology reduces variability and technical errors and cost of single-cell omics studies.
Common applications are single cell processing for:

  • mRNA sequencing
  • Targeted gene expression
  • mRNA expression profiling
  • Whole genome sequencing
  • Targeted DNA sequencing

Post-C1 processing is performed in the LRI Genomic Core


The ZetaView is a nanoparticle tracking analyzer to determine the size histogram and concentration of exosomes and microparticles in biological fluids. The detection range is 10nm-20µm.