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Berkeley Lab Biosciences FACS Facility


The Biosciences FACS facility consists of a Becton-Dickinson FACSVantage SE high speed cell sorter, and a FACSCalibur flow cytometer. The facility was established by the Life Sciences Division; the mission of the facility is to support biosciences research at Berkeley Lab by providing capabilities which individual labs might not otherwise have access to.

The facility is managed by Michelle Scott (room 977-118, ext.4281, e-mail) along with backup support provided by flow cytometry experts from the UCSF Lab for Cell Analysis (LCA), Sarah Elmes and Bill Hyun. Berkeley Lab oversight of the facility is provided by Sylvain Costes.

For training and most questions, contact Michelle Scott. She is available in person at the facility during normal work hours.

Getting Access

The facility is available to all Berkeley Lab reseachers with valid Berkeley Lab employee or affiliate appointments, and who have access to a valid Berkeley Lab project ID for the usage charges. The systems are located in the Berkeley West Biocenter (a.k.a. Potter Street) in room 116. After completing training users may use the analyzers; and after very extensive training they may use the sorter. Training sessions can be scheduled by emailing Michelle. As part of the training users will be asked whether they completed the relevant EH&S training and whether the use of the FACS facility has been documented in the Biological Use Authorization (BUA) for the home lab of the user. Access to the FACS facility is prohibited until completion of instrument training, EH&S training, and BUA documentation. See EH&S information below for more detail on these issues.

Once trained, users can sign up for and use the systems for which they completed training. Sign up through, selecting the Lawrence Berkeley Laboratory Cytometry/Microscopy facility. For instructions on how to add this schedule to a Google or Outlook calendar, see this document.

In order to log in on the computer that controls the FACS instrument, an account is needed on Berkeley Lab's Active Directory or Windows Domain system (Note: This is different from the LDAP account that is used for email, LETS, etc.). Many Berkeley Lab users already have an account and can simply use that to log in. If not, visit this site to request a Windows Domain account. See here for more information about Active Directory.

Read the section below for information about usage charges and supplies.

Usage Charges & Supplies

Currently the charge for any instrument is $25.00 per hour. Also, if operator assistance is needed an additional fee of $120.00 per hour is charged. (Fee schedule)

Users are charged via the Facility Online Manager (FOM) system. Please download and read the instructions for setting up an account.

The facility provides sheath fluid and cleaning solutions for each cytometer. All other supplies must be brought by the users. This includes slides, transfer pipettes, gloves, etc. which can be purchased from VWR. In the resources section below is a list of the typical supplies and the ordering information.

EH&S Information

The FACS facility is located in a BSL-2 lab; no food or drink is allowed. Each user must have completed and be current on the following EH&S training: EHS0735/738 Bloodborne Pathogen training and annual refresher, EHS0745 Hepatitis B Medical Surveillance training, EHS0604 Hazardous Waste Generator training, and EHS0730 Biohazardous Waste training. Visit the EH&S training website for more information. The use of the FACS facility and the method of transport of samples between the home lab and the FACS facility must be documented in the BUA of the Principal Investigator. To facilitate this an EH&S-approved insert is available that can be made part of the Principal Investigator's BUA. If you have any questions about this insert, please contact Sylvain Costes (email) for information. In addition, every FACS user should be familiar with the Standard Operating Procedure document. Ensuring that all EH&S regulations are properly followed is the responsibility of the user and their Principal Investigator.

Data Storage and Analysis

The computers that control the FACS machines may temporarily be used to store acquisition data; these will be kept for one week after acquisition. Users are responsible for their own data and can copy it over the network to their lab's server, copy it to a USB memory stick or portable USB hard drive, or burn it onto a CD or DVD. For flow data analysis the FlowJo program is recommended which can be made available for a reduced fee through a collaboration with UCSF. For an annual (July 1 through June 30) fee of $150 a license code is provided to run the program on the user's own computer (PC or Mac). Simply download the FlowJo program, install it, and run it in evaluation mode. Once ready to purchase, contact Sarah Elmes for further information.

FACSVantage SE

FACSVantage SE image

The FACSVantage SE is a digital high speed cell sorter, configured with three lasers:
1.   488 nm Blue-green solid state laser
2.   405 nm Violet solid state laser
3.   635 nm Red solid state laser
Four fluorescence channels and two scatter channels are available from the 488 nm laser (FSC, SSC, FL1, FL2, FL3, FL4).
Two fluorescence channels are available from the 405 nm laser (FL5, FL6).
Two fluorescence channels are available from the 635 nm laser (FL7, FL8).
Nozzle sizes from 50 to 400 micron are available depending on cell size.
Direct sorting into 5 ml and 15 ml tubes and direct cloning into 96-well plates are available.

FACSVantage SE Quick Guide (Note: training is required)


FACSCalibur image

The FACSCalibur is a bench-top cell analyzer, configured with two lasers:
1.   488 nm Blue-green Argon Ion laser
2.   633 nm Red Helium Neon laser
Three fluorescence channels and two scatter channels are available from the 488 nm laser (FSC, SSC, FL1, FL2, FL3).
One fluorescence channel is available from the 633 nm laser (FL4).
An optional High Throughput Sampler station is attached to allow direct sampling from 96-well and 384-well plates.

FACSCalibur User Instructions (Note: training is required)


EH&S Approved Insert
Facility Online Manager (FOM) account set up instructions
FACS schedule--how to add to Google or Outlook calendar?
FACSCalibur User Instructions (Note: training is required)
FACSVantage SE Quick Guide (Note: training is required)
Google Drive, containing instrument manuals, user guides, etc.
Shopping List
Standard Operating Procedure document

Contact Us

If you have any questions about the FACS Facility, please contact Michelle Scott in room 977-118, ext. 4281, or via e-mail.


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Last updated: 07/11/13