Services

Overview:  The Flow Cytometry Core provides 13 main services and 10 different instrument types listed below, consisting of various core technologies including flow and mass cytometer analyzers, flow cytometer cell sorters, single cell genomic isolators, genomic analyzers, genomic library preparation equipment, as well as analysis work station and software options for analyzing your data. In addition, we also offer guidance and assistance services to help you utilize the instruments to their full potential. Instruments with the "self" prefix indicate that you can be trained to use them yourself.

  1. Self analysis on Flow Cytometers | Analyzers
  2. Self sorting on Flow Cytometers | Cell Sorters
  3. Operator Assisted Cell Sorting
  4. Self analysis on Mass Cytometer | CyTOF
  5. Operator assisted analysis on CyTOF
  6. CyTOF Antibody Conjugation
  7. Self Genomic operation of Fluidigm platforms
  8. Assistance / Guidance
  9. Training
  10. Analysis Workstations / Software

*** Please be aware there are certain limitations and new guidelines due to COVID-19 pandemic. Please visit our for the latest information regarding the guidelines and support during the COVID-19 pandemic . **

 

This LINK contains the configurations of all instruments in the Core. 

The Summary Table will provide a matrix of all the key features of each instrument.  Click on the nickname link of a specific instrument to get a more detailed layout.  Tabs are also at the bottom listing the machine nicknames. It is essential for planning your experiments and seeing if an instrument can detect your specific markers.  If you need to download a copy, click on "File" then "Download as" from the Google menu. Please contact us if you have any questions or are in need of a specific filter set for your experiments.    

Click on any link in the section below for more information on each instrument/service.

Click HERE to check Instrument Status of the systems in the Core.


Self analysis on Flow Cytometers | Analyzers

FACSCalibur

"Gonzo the Great"

Up to 2 size & 4 fluorescent parameters. Click HERE for details.

 

LSRII / Fortessa / X20 

"Big Bird", "Kermit", "Oscar the Grouch", "Cookie Monster", "Grover", "Bert", "Ernie"

Up to 2 size & 18 fluorescent parameters. Click HERE for details.

 

FACSymphony

"Stay Puft Marshmallow Man"

Up to 2 size & 28 fluorescent parameters. Click HERE for details.

Luminex 100 (BioPlex 200)

"The Count"

Up to 2 fluorescent parameters. Click HERE for details.

  • Analyzer only.
  • Plate mode for multiplexing is standard. 
Nanosight NS300

"Skipper"

Small Particle analyzer. Click HERE for details


Self sorting on Flow Cytometers | Sorters

FACSAria

"Animal", "Beaker", "Boo Boo" , "Bunsen Honeydew", "Yogi Bear", "Jabba the Hutt", "Mylo"

Up to 2 size & 18 fluorescent parameters. Click HERE for details.

  • Can sort up to 4 different populations.
  • Can sort into plates up to 384 wells.
  • Can index sort.
 
 
Sony SH800

"Crash Bandicoot"

Up to 2 size & 6 fluorescent parameters. Click HERE for details.

  • Can sort up to 2 different populations.
  • Can sort into plates up to 96 wells.
  • Can index sort.
  •  Much easier to setup than other sorters.

 


Operator Assisted Cell Sorting

Service available to request for any Cell Sorter by requesting Assistance Service.

 


Self analysis on Mass Cytometer | CyTOF

CyTOF - Helios

"Charmander" and "Blue"

Up to 48 heavy isotope parameters. Click HERE for details.

  • Analyzer only.
  • Can be run using syringe mode or 
  • Super Sampler.

 

Operator assisted analysis

coming soon

 

 

Antibody Conjugation

coming soon

 


Self Genomic operation of Fluidigm platforms

Isolation C1 

"Stich"

  • Capture single cells. Isolate their individual genomic content.
  • Available to use now. More details coming soon HERE 
Analyzer Biomark

"Sully"

  • Available to use now. More details coming soon HERE
Library Prep Access Array

"Minions"

  • Available to use now. More details coming soon HERE

 

Guidance

Overview:  The Guidance service is requesting a Flow Core staff member to help you become more familiar with the instrument after the initial training. Following training, Flow Core staff will guide you while running your first few experiments, or if you want us to look over your instrument settings.

Availability: Monday-Friday, 8am-7pm. You must schedule as soon as you make the instrument reservation and provide at least 1 week notice. 

Guidance can also be requested if you need staff to review your instrument settings while you are setting up the instrument or any other general instrument questions. This differs from the Core's Assistance service, as the Guidance service has no charge associated with it. External users do not have this option and must request the Assistance service for their Guidance.

Here is how to submit the request: Scheduling Guidance

The Core also offers Assistance service if you are looking to run an experiment before completing your training.

Assistance

Overview:  The Assistance service is requesting a Flow Core staff member to be at a specific instrument to run your samples for you. Assistance can also be requested if you need instrument setup on weekends, holidays, and non-normal work hours (Monday-Friday from 6pm-8am at standard rate).

Availability: Monday-Friday, 8am-6pm. You must schedule as soon as you make the instrument reservation and provide at least 1 week notice.

The Core may charge double the Assistance rate if a request is made to operate and run samples on weekends, holidays, and non-normal work hours. This differs from the Core's Guidance service, as the Guidance service has no charge associated with it and is useful for users who need a bit of help when running their own samples and checking their instrument settings.

Here is how to submit the request: Scheduling Assistance

 


Training

UCSF Flow Training Program, click HERE

 

 


Analysis Workstations and Software packages

Overview:  The Core provides computer work stations allowing analysis of cytometry data.

Availability: 24 hours, 7 days a week.

In addition to flow cytometry analysis software, all computers contain copies of Microsoft Office as well as Adobe Photoshop and Illustrator allowing the generation of figures for meetings and papers. Check out what the computers are equipped with and contact us if you have any questions about them.

To schedule time on the Workstation please use our Scheduling system.

All the software below can open FCS files from any cytometer.

FCS Express: A powerful analysis option, analyze the FCS, plot graphics and perform statistical analysis on one platform. It can be a bit of a learning curve to utilize all the features.  If you want your own copy and you are a UCSF internal/affiliate employee, click HERE to view instructions to request license.

  • Contact [email protected] with any questions
  • There is an annual rate associated for 1 license; registrations are valid through the end of the license term (April 30). After May, billing occurs at the end of each cycle; please ensure you provide a speedtype which will be valid at the time of billing and make sure to notify your finance administrator. 
    • Register May 1 - October 30: full rate
    • Register November 1 - April 30: half rate

FlowJo:  A powerful option, but can be a bit of a learning curve to utilize all the features.  If you want your own copy and you are a UCSF internal/affiliate employee, click HERE.

FACSDiva:  The PCs contain this acquisition and analysis software allowing the importing of experiments from BD instruments such as the LSR/Fortessa/X20/Symphony/Aria class of instruments which can save time by not having to redraw gates.  Can be a timesaver when making slides for a lab meeting or conference.

Kaluza:  A very user friendly, yet powerful analysis software from Beckman Coulter.  Requires a software dongle to use.

CyTOF Software:  Can be used to create templates for your panels which can be exported to the instrument computer.  Can also provide data concatenation as well after data acquisition.  If you want your own copy, you'll need to create an account on their website before downloading.

UCSF Cytobank:  Can be used to analyze any type of FCS file and has various algorithms to interpret high dimensional data.  Highly recommended for analyzing files off the CyTOF and high parameter flow cytometry data.  Cloud based and can be used anywhere as long as you have an internet connection.  If you want your own license seat, first 30 days are free, and after $1,500/year.  The Core provides access to 1 shared account which can be used for free by UCSF researchers.  You must sign up on the MyCores online scheduler to use this shared account, so other people don't get kicked off.  See Cytobank's website for more info.

Amnis IDEAS Software:  Used for analyzing data off the Amnis Image Stream.

PFCC and RRP provides access to several site licenses for:
  • FCS Express, click HERE to register for a license.
  • FlowJo, click HERE for details

This LINK contains the configurations of all instruments in the Core.