Flow Cytometry Core

Safety Information

Salk Institute for Biological Studies - Flow Cytometry Core - Safety Information


FCCF is a multi-user core facility, and the safety of staff, users and visitors is of paramount importance. The facility may contain biological, chemical, laser, and other hazards. This document outlines many of these hazards and provides a reference for operating procedures. Users are reminded that they must also adhere to the posted Institute safety regulations at all times.

Laser Hazards
Lasers are used in many of our instruments. With few exceptions, these machines include hard-to-disable safety devices, which prevent user exposure to the beams in normal use.

The cell sorter contains two class IV argon-ion lasers capable of producing a visible beam power in excess of 5 Watts, or an invisible ultraviolet beam in excess of 200 milliwatts. Even at standard operating powers of a few hundred milliwatts, these devices are potentially very dangerous. During machine alignment, it is often necessary to direct an exposed beam at a target in the flow cytometry lab. When this procedure is being carrried out, FCCF staff will close the laboratory door and post a warning sign. Eye protection must be worn by anyone present in the lab. While the sorter is operating, no-one except trained personnel may open any of its covers or proceed behind the instrument.

The analytical flow cytometers only present a laser hazard if the safety covers are removed or the interlocks are defeated. It is relatively easy to defeat the FACSCan safety shutter when examining the flow cell, and users must not do this.

Biological Hazards
Many different samples from various sources are brought into the facility. Some of these may contain known, unknown, or potential, pathogenic agents. Because many investigators visiting the Core work with rodents, agents which may be hazardous for animals are viewed in the same light as those which may be hazardous for humans.

No room in the FCCF facility is equipped to handle any material greater than biosafety level 1 (BSL1). A BSL1 organism is defined by the CDC Office of Heath and Safety as presenting minimal potential hazard to healthy adult humans and the environment.

The laboratory presenting the greatest biological hazard is the flow cytometry laboratory, because samples are often open and may spill or create aerosols. The analytical flow cytometers have a droplet containment mechanism to minimize aerosol generation, however vortexing an open sample will generate aerosols even before the sample is introduced into the cytometer. The cell sorter is a jet-in-air device and generates copious quantities of aerosols. There are specially rigorous restrictions on what may be handled by this machine.

  • Lentivirus and adenovirus: The hazards associated with lentiviral and adenoviral vectors are not well defined; the flow cytometry community is working to establish rigorous guidelines for such agents.
  • Analysis: If your sample contains lentivirus, adenovirus, or any other genetically engineered amphotropic virus, it may be analyzed provided you treat it as a BSL2 hazard (recommended by Invitrogen). This means that it must be kept closed at all times except when being put onto the cytometer’s sample introduction port. You may not vortex an open tube, and if you do vortex a closed tube, take great care when opening it and point it away from yourself and anyone else. When you are done running samples, you must decontaminate the machine by running a fresh 20% solution of bleach for 5 minutes, followed by two changes of deionized water for 2 minutes each. You must also decontaminate your work area by wiping with 70% ethanol.
  • Sorting: Because of sorter aerosol generation, you may not sort lentivirus or adenovirus infected cells unless you can conclusively demonstrate that there is no free virus in the system. For lentivirus, this is generally true if there have been at least 7 culture passages after infection. If you have used the viral vector to introduce potentially hazardous elements into the cells (e.g. oncogenes), they may not be sorted.

For more information, see the CDC publication: Biosafety in Microbiological and Biomedical Laboratories and the Canada PHA publication: Laboratory Biosafety Guidelines . Also see: Statement of the Swiss Expert Committtee for Biosafety on the classification of work with genetically modified viral vectors (PDF document).

Chemical Hazards
Chemical hazards exist in most areas of the facility and include, but are not limited to, acids, alkalis, organics and mutagens.

Other Hazards
As with any laboratory, the facility contains many other common hazards, particularly electrical, which will not be discussed here in any detail.