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 Shared FACS Facility FAQ

How do I add a new Project with Biosafety information?

1.  Add a project to your FACS account information -, click 'Account Info':

  • Include cell type, any pathogen or recombinant DNA constructs and viral transduction systems used
  • Include any fixation protocol, if applicable
  • Sorting must be specified, if applicable
  • APB information (APB number, expiration date) must be included, if applicable

2.  Email a highlighted copy of the relevant APB, please highlight:

  • The source of the samples,
  • Any pathogen, recombinant DNA treatments (lentivirus, plasmids, etc)
  • If lentivirus, or similar, include exact transduction system/generation
  • Highlight the portion of the APB showing where you have been added to the protocol
  • Highlight the portion of the APB showing the samples will be analyzed at the FACS facility.
  • The fixation method must be included and approved by EHS as being adequate for virus/pathogen inactivation

Sorting at the FACS facility must be explicitly approved for your samples in the APB - if not currently included, contact EHS, this is a minor modification and typically processed quickly

How do I book time with an operator?

After you have registered, staff will review the submitted BSL-2 information for your projects.  Once your BSL information is reviewed by the staff you can access and book staff-assisted instrument time on any of our instruments.  Timeslots with available operators will appear as green on the instrument calendars.  If the desired appointment is not available with a single operator, a message will display indicating the last time available - this indicates the appointment selected requires more than one operator.  Click OK, then simply book a second appointment for the remaining time and the second slot will be assigned to the next operator.  Please reserve sufficient time for both setup and cleaning. 

How much time should I reserve?

Allow sufficient time for setup, sample analysis/sort, and for cleanup.  The operator must stop with sufficient time to clean the instrument before the next user.  Complete cleaning is MANDATORY.  Failure to adequately follow cleaning procedures will incur additional charges (instrument + staff) of 30-60 min, depending on time required to restore optimal instrument performance.  After the 3rd infraction, user status will be changed to staff-assisted and independent operation of facility instruments will not be allowed. 
Minimum time guidelines for staff-assisted appointments are below:
Analyzers (30min minimum appointment):
-SETUP:  5 minute QC and setup PLUS time to run compensation controls and set up template (~5-10min)
-CLEANUP:  Minimum of 10 minutes cleaning time.
Sorters (1 hour minimum sort appointment time):
-SETUP:  15 min plus time to run compensation controls and setup template (10-15min, can be longer if many comp controls or low bead/cell numbers)
-CLEANUP:  Minimum of 15 min. for sorters, if running human or infectious samples (or yeast or bacteria) BSL-2 cleanup on sorters requires 25min

How do I know what machine to book?

The configuration of each instrument, including lasers, and standard detector filters can be viewed on the website.  If you are new to flow cytometry, or have additional questions, you can book a consultation appointment to discuss your experiment(s).

What happened to my files?

All experiment files are uploaded to Stanford Medicine Box SSFF Archive as a single zip file.
For users with a PC, the native extractor program has trouble reading the zipped file's header information and you will see an error:  'File not valid', or something similar.  Simply download the free 7-zip program (, install, and use to unzip the files. To do this, right-click and select 'Extract with 7-zip'.
For users with Mac OS 10.14 (Mojave) or lower, the native file extractor on the Mac will unzip the experiment folder without a problem.
For Macs running MacOS Catalina 10.15.2 or higher, zip files can be extracted using the free application Zip File Unarchiver available in the Mac App Store.

How do I get trained to run the analyzer or sorter myself?

To request training on the instrument, you must first be a fully registered user.  Once your regsitration is complete, navigate to Education & Resources, Book Training.  This page contains all the details and instructions needed to train as a self-operator on each type of instrument.


How do I request after hours use?

After you have been an independent user for a reasonable amount of time (always >20h independent operation), email the director to review troubleshooting and apply for afterhours access. After hours use approval is considered on a case by case basis.

Sorting FAQ


What do I need to bring to my sort  appointment?

  • Samples:  pre-filtered through a 40 micron mesh
  • Vessel(s) to collect into with fluid (buffered media) already in it.

What should I sort into?

  • You can collect into 0.5 or 1.5 ml Eppendorf tubes, 5ml 12x75 tubes or 15 ml Falcon tubes OR into plates (6/12/24/96/384)

What density should the cells be at?

  • Cells should be at ~20-40 million/ml. Bring extra buffer to dilute the sample in case it's too concentrated.

How many populations can I collect at once?

  • The Aria sorters can sort into (2) 15ml or up to (4) Eppendorf or 5ml facs tubes at one time. They are designed to collect only one population at a time for any of the plate configurations.
  • The Sony sorter can collect 2 populations at one time into tubes, one population into plates.
  • The Influx sorter can collect up to 6 populations at one time into Eppendorf or 5ml facs tubes.

Which sorters can collect into 96 and 384 well plates?

  • All of the sorters at our facility can sort into 96 and 384 well plates.
  • The Satchmo, Mikado and Carmen are best for sorting into 384 well plates.
Last modified: 
Thu, 7 Sep 2023 at 12:38 pm