Flow Cytometry

Providing access to high-speed cell sorting and analytical flow cytometry.

Flow Cytometry Equipment


The facility provides access to high-speed cell sorting and analytical flow cytometry in two locations on the Sanford Burnham Prebys campus. Trained investigators have 24-hr/day access to a variety of analytical flow cytometers available for independent use. Core staff provide technical expertise, hardware and software training, operate the facility’s cell sorters and are available to assist with analysis experiments for those who prefer to have their samples run by an expert cytometrist.

Scientists planning a flow cytometry experiment are encouraged to consult facility staff for assistance with protocols, fluorochrome selection or other aspects of experiment design. Sorter and analyzer optical configurations can be viewed here.


High speed cell sorting

  • Expertise in calcium flux, cell cycle, side population, and sorting of IPSC and ESC, tumor progenitor and tissue stem cells
  • Performed by facility personnel in two locations
  • Single-cell (clone) sorting into 96 or 384-well plates
  • Simultaneous sorting of up to 4 populations
  • BSL2 biosafety enclosures

Analytical flow cytometry

  • Consultation
  • Experiment design
  • Hardware and software training
  • Do-it-yourself 24hr/day, or assisted by appointment up to 14 colors with plate loader
  • Data analysis and interpretation
  • Publication quality figures
  • Assistance with methods sections
  • Pre-publication manuscript review

Equipment & Resources

  • Amnis ImageStreamX MarkII imaging flow cytometer
    • 12 imaging channels (10 colors and 2 brightfield channels)
    • 405 nm, 488 nm and 642 nm laser lines
    • 20x, 40x and 60x objectives
    • 96-well plate loader
    • Extended Depth of Field (EDF) option for spot counting
    • Inspire acquisition software
    • Ideas analysis software
  • Computer workstations (Macintosh OSX) with large monitors and data analysis software packages including
    • FlowJo
    • ModFit LT
    • FACSDiVa
  • Acea NovoCyte 3000 13-channel flow analyzer
    • 488nm, 405 nm and 640 nm lasers
    • Multi format autosampler
  • BD FACSAriaIIu 16-color high-speed cell sorter
    • Four solid state lasers (405 nm, 488 nm, 561 nm, 640 nm)
    • BSL2 containment
    • Sort into tubes or plates
  • BD LSR Fortessa X20 18-color FACS Analyzer
    • Five solid state lasers (488nm, 637nm, 405nm, 561nm and 355nm)
    • BSL2 containment
  • BD FACSCanto 6-color FACS analyzer
    • 488 nm and 633 nm lasers
    • Typical fluor combinations: FITC, PE, PerCP, PE-Cy7, APC, APC-Cy7 or equivalent
  • BD LSRFortessa 14-color FACS analyzer
    • HTS plate loader for 96 or 384-well plates
    • Four solid state lasers (405 nm, 488 nm, 561 nm, 640 nm)
  • BD FACSAria 15-color high-speed cell sorter
    • Four solid state lasers (405 nm, 488 nm, 561 vnm, 640nm)
    • BSL2 containment
    • Sort into tubes or plates
  • BD FACSCalibur 4-color analyzer
    • 488 nm and 635 nm lasers
    • Typical fluor combinations: FITC, PE, PerCP, APC or equivalent

Price List

For a complete list of services, please call (858)646-3100 ext. 3569 or email us.


Flow Cytometry Services Internal Subsidized Internal External Non-Profit External For-Profit
FACSAria Setup each $38 $47.50 $51.30 $99.94
FACSAria Sorting hour $75 $93.75 $101.25 $197.25
ImageStreamX II Assisted Use hour $60 $75 $81 $157.80
ImageStreamX II Independent Use hour $25.50 $31.50 $34.02 $66.28
LSRFortessa Independent Use hour $34.80 $43.50 $46.98 $91.52
LSRFortessa Training hour $64.80 $81 $87.48 $170.42
LSRFortessa + Staff Operator hour $67.80 $84.75 $91.53 $178.31


Facility Director
Scientific Director
Senior Flow Cytometry Specialist


The flow cytometry core staff has more than 18 years of cell sorting and flow cytometry experience in NCI-designated Cancer Center core labs.

Yoav Altman

Yoav Altman received his BA degree in Integrative Biology from the University of California at Berkeley. He started working with flow cytometry in 2001 at La Jolla Institute for Allergy and Immunology and joined Sanford Burnham Prebys Medical Discovery Institute in 2002 as Manager of the Flow Cytometry Shared Resource. He was promoted to Director in 2009, and oversees the operation of both core lab locations. Yoav is the primary operator of the FACSVantage DiVa cell sorter in building 5 and trains investigators to use the core's cytometers. Yoav has over ten years of experience sorting a variety of cell lines and primary cells including IPSCs, hESCs, immune cells, disaggregated tumors and solid tissues such as cardiomyocytes, hepatocytes, intestinal epithelium, brain tissue, and skeletal muscle. Over this time he has worked with a variety of single cell assays including side population, cell cycle, apoptosis determination, immunophenotyping, calcium flux, mitochondrial membrane potential, ROS, fluorescent proteins, and FRET. Yoav is available to assist with reagent selection, experiment design, data analysis, protocol development, grant preparation, and writing methods sections for publications.

Amy Cortez

Amy Cortez first trained in Flow Cytometry at the MD Anderson Cancer Center in Houston TX in 2007 where she became proficient in cell sorting and flow cytometric analysis of cell viability, intracellular and cell surface antigens, and the effects of cancer treatment. She joined SBP Flow Cytometry Core in 2010 where she continues to expand her knowledge of multicolor analysis and sorting, while offering management assistance to the director of the core. Amy’s six years of molecular biology research experience using techniques such as PCR, Western Blotting, sequencing, and SNP analysis enable her to understand the scientific needs of the investigators that come through the core. Amy is the lead operator of a 15-parameter FACSAria cell sorter.

Please call (858)646-3106 or use the button below to send us an email.

Contact the Facility