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Shared Resources

Flow Cytometry



The speed at which the automated instruments of this resource can examine or separate free floating cell populations for several parameters - sometimes simultaneously - and chart the results, provides powerful opportunities for obtaining data on cell populations of statistically reliable size.


Flow Cytometry Shared Resource Services

Service Profile

  • Aseptic sorting of living cell populations (up to 4 simultaneous collection tubes)
  • Direct cloning into microtiter tissue culture plates or onto microscope slides
  • Isolation of rare cell subpopulations or large number of cells
  • Quantitative fluorescence analysis (up to 9 colors)
  • Consulting (design of experiments; analysis or conversion of data)
  • Typical applications include:
    • Viability and toxicity assays
    • Apoptosis assays (TUNEL, sub-G1, caspases, Annexin V, mitochondrial membrane potential, etc)
    • Calcium Flux
    • Intracellular pH
    • Degranulation
    • Oxidative Burst
    • Phagocytosis
    • Reticulocytes
    • Platelets
    • Bead-based assays

Service Details

  1. Analytical Flow Cytometry Utilizes a Becton Dickinson FACSCalibur, a 4-color, dual-laser benchtop flow cytometer. Included is the CellQuest software for list-mode data recording and analysis. Data recording and analysis can be performed with the FACS Aria, a triple-laser, multiparameter flow cytometer using up to 11-color fluorescence signals, along with forward and side-angle light scatter.
  2. Cell Sorting In addition to analytical experiments, the FACSAria can perform aseptic sorting of living cell subpopulations utilizing various criteria, such as intrinsic cell properties, e.g. DNA content, Green Fluorescent Protein (GFP), or extrinsic properties, such as molecular markers identified by fluorescently-labelled monoclonal antibodies.
  3. Automated Magnetic Cell Sorting (autoMACS) Used for convenient isolation of rare cell subpopulations or large numbers cells, up to 4 x 109. Its use of magnetic particles for cell separation is both useful and efficient, and the cells can then go straight to FACS analysis or further sorting. Manufacturer's website: autoMACS
  4. Consultation In addition to education about the functionality and capabilities of the Shared Resource, technical support personnel also advise in the design of experiments and assist investigators in the initiation of pilot projects, provide limited amounts of specific reagents, and contribute detailed consultation in analysis of data.


  • Toxicity and viability assays (PI, NK assays, CTL, etc.)
  • Many apoptosis assays (DNA content, TUNEL, SBIP, Annexin-V, caspases , mitochondrial membrane potential, etc.)
  • Quantification of cells expressing specific surface, cytoplasmic, secreted, or nuclear antigens
  • Proliferation assays (BrdU, PKH-26, CFDA-SE etc.)
  • Cell Cycle Analysis (by quantification of DNA or incorporation of BrdU)
  • Separation of living cell populations expressing marker genes for specific cell lineages (GFP, FACS-gal, NGFR, etc.)
  • Cloning of cells modified by introduction of novel genes for therapeutic purposes (CloneCyt Plus)
  • Calcium Flux (Fluo-4, Fluo-3/Fura Red, Indo-1)
  • Membrane Potential
  • Enzyme Activity
  • Glutothione Determination (CellTracker, NDA, etc.)
  • Multidrug Resistance (MDR) Assays
  • Intracellular pH (SNARF-1)
  • Phagocytosis (HDCF-BSA, Dihydrorhodamine 123, calcein, bacteria, yeast etc.)
  • Oxidative Burst, Free Radicals & Reactive Oxygen Species
  • Degranulation & Actin Polymerization
  • Quantification of Reticulocytes
  • Cytometric Bead Arrays
  • Platelet Activation
  • Aseptic sorting of any subpopulation of cells from suspension into tubes or microtiter culture plates or directly onto slides
  • Index Cell Sorting: The well location is identified and recorded when a cell is sorted, making correlation of flow cytometry data (e.g., fluorescence intensity) with non-flow based assays more accurate.


  • BD FACSAria (High speed, 9-color, tripe-laser cell sorter)
    • Automated Cell Deposition Unit (ACDU)
    • 4-way sorting
  • BD FACSAria II SORP (High speed, 13-color, 4-laser cell Sorter)
    • Automated Cell Deposition Unit (ACDU)
    • 4-way sorting
  • BIO-RAD S3 (2-laser, 4-color cell sorter)
  • BD FACSCalibur (2) - 4-color, non-sorting cytometers

Flow Cytometry Links

Recharge Rates

​Item Code
Item Description
​Unit Cost
FC0003A1Flow Cytometer Use/hr. (Sorting) - Participating Member
FC0003A2Flow Cytometer Use/hr. (Sorting) - Associate Member
FC0003BFlow Cytometer Use/hr. (Sorting) - Non-Member, UCSD Faculty
FC0003C1Flow Cytometer Use/hr. (Sorting) - Non-University, Non-profit
FC0003C2Flow Cytometer Use/hr. (Sorting) - Non-University, For-profit
FC0003C3Flow Cytometer Use/hr. (Sorting) - Cancer Centers Council
FC0004A1Flow Cytometer Use/hr. (Analysis) - Participating Member
FC0004A2Flow Cytometer Use/hr. (Analysis) - Associate Member
FC0004BFlow Cytometer Use/hr. (Analysis) - Non-Member, UCSD Faculty
FC0004C1Flow Cytometer Use/hr. (Analysis) - Non-University, Non-profit
FC0004C2Flow Cytometer Use/hr. (Analysis) - Non-University, For-profit
FC0004C3Flow Cytometer Use/hr. (Analysis) - Cancer Centers Council
FC0005A1Flow Cytometer Use/hr. (Self) - Participating Member
FC0005A2Flow Cytometer Use/hr. (Self) - Associate Member
FC0005BFlow Cytometer Use/hr. (Self) - Non-Member, UCSD Faculty
FC0005C1Flow Cytometer Use/hr. (Self) - Non-University, Non-profit
FC0005C2Flow Cytometer Use/hr. (Self) - Non-University, For-profit
FC0005C3Flow Cytometer Use/hr. (Self) - Cancer Centers Council


Operating Policies

Please contact Thomas Kipps for more information.


Thomas J. Kipps, MD, PhD
Professor of Medicine

Dennis Young
Phone: 858-822-0407
Fax: 858-822-0407

UC San Diego
Moores Cancer Center
3855 Health Sciences Drive
MC 0803
La Jolla, CA 92093-0803
Room 2317-Q