Salk Institute
Flow Cytometry Core Facility

Using the Flow Cytometry Core Facility

The following is basic information to help new users understand how to use the various FCCF services. Please also read our safety notices.

Getting started at FCCF: Create yourself a *PPMS account; users of the Biophotonics Core already have a PPMS account set up:

  • Scheduling and Rates → Account Request

You will need to provide your Fund #, for recharging purposes - ask your supervisor/lab manager for this. Please note also that resource schedules are only activated after your access has been approved following training with FCCF.

For analysis, bring samples ready to run at FCCF in Falcon 2052 tubes. Samples for sorts: use sterile capped tubes eg. 352003, or 352235 (filter tops) for convenience.

Analytical Flow Cytometry Instrumentation

FCCF has bench-top analyzers available for independent operation. Contact the facility for advice on experimental design and instrument selection.

New users: If you are new to the technology, review the short introductory courses listed below before contacting FCCF for instrument training:

Request training via PPMS well before setting up an experiment as the cytometers have different capabilities; we want to verify your fluorochrome choices are compatible as well as ensure you have optimal experimental design before money is spent on reagents (i.e. fluor/probe selections and combinations).




FACScan (1- laser, 3 color)


Small number of relevant experimental samples (discuss your experiment first with facility staff)

LSR II (5 laser, 15 color)

2 hours

Beads will be provided for training.

Post training support: Keep your first few experiments simple while you are learning to run an experiment unassisted, and please coordinate with us during this initial phase so we can support you if needed - we want your experiments to be successful. 

Fluorescence Activated Cell Sorting (FACS)

The Flow Cytometry Core Facility has a multi-laser Becton Dickinson FACS Vantage SE DiVA cell-sorter, which is operated by staff. Depending on your needs and scheduling availability, it may take up to 1 week to accommodate you.

Sort Requests: Contact us well before you set up your experiment so that we may discuss your exact requirements. You may do this through PPMS.

Note: Some cells are more fragile than others, and your samples are important to us: we will optimize instrument set up to achieve the best sample recovery for your individual needs.

Sample preparation is critical for the success of your sort and to minimize down time due to a clogged sort nozzle; this is discussed further in the section called Sample Preparation.

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