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Single cell analysis using flow and mass cytometry, 3 credits.

Singel cell analys med hjälp av flödes och mass cytometri, 3 hp.

Entries/Anmälan Application deadline 15 April 2018


Time: 15-31 May (weeks 20-22) 2018


To qualify for studies on third-cycle education courses, you must have a:

  • second-cycle degree,

  • 240 credits in required courses, including at least 60 second-cycle credits, or

  • acquired equivalent knowledge in some other manner

For this course you are also required to have experience of multi-parameter flow cytometry.


Priority will be given to those who have a planned and/or on-going mass cytometry project.



Learning outcomes

After completing the course the students will be able to:



  • Understand how a mass cytometer works

  • Know the pros and cons of flow and mass cytometry

  • Be able to choose which of these methods is best suited to answer the specific scientific question

  • Understand the background when designing a mass cytometry experiment

  • Have been introduced to different analytic software such as ACCENSE, SPADE, viSNE and Citrus which enable evaluation of data collected by mass cytometry


Participants will have the ability to plan mass cytometry experiments on a detailed level and be able to decide which analytical software to use on acquired mass cytometry data.




Flow cytometry is the method of choice when single cell multiplex analysis of protein receptors are to be examined with fluorochrome labeled antibodies. Unfortunately problems with spectral overlap occur from the different fluorochromes necessitating color compensation. This will in practice restrict experiments to analyzing only 12-16 proteins on a single cell level.

A mass cytometer or Cytometry by Time-Of-Flight (CyTOF), however, has the capacity to analyze up to 40 proteins at a single cell level. This is made possible by utilizing rare earth metals conjugated to antibodies instead of fluorochromes. The different masses of the individual metals are easily detected by the time-of-flight mass spectrometer thus rendering the need for compensation unnecessary.


The course will include lectures concerning;

An introduction to single cell analysis at protein level.

Basic principles in flow cytometry.

Basic principles in mass cytometry.

The CyTOF2 instrument.

How to design a panel of metal tagged antibodies.

Presentation of different multi-parameter analysis software.

Introduction on how to use one analysis software.

A demonstration of the CyTOF2 instrument will be given.


Educational methods


The pedagogical approach applied at the Faculty of Medicine and Health Sciences is student centered, problem based learning (PBL). The student takes responsibility for his/her own learning, and seeks and evaluates information and knowledge based on own queries and formulated problems. The role of the teacher is to guide and support the students.


Educational methods applied in this course are seminars held by both in-house speakers and invited experts within different areas. Participants will be given home-assignments and the results will be presented to the group. A demonstration of a mass cytometry experiment will be held in smaller groups.



Presence at all seminars is required. Participation in discussions will be evaluated.


Students who fail are offered one re-examination occasion in close connection to the course.  The re-examination will be equally comprehensive as the ordinary examination.


Change of examiner

Students who have failed the course or part of the course twice are entitled to request another examiner for the following examination occasion.



Pass or Fail.


Course certificate

 A course certificate can be issued by the course coordinator if requested by the student.


Recommended reading

The course coordinator will provide a list of relevant literature before the start of the course.


General information

The course is planned and carried out according to what is stated in this syllabus. Course evaluation, analysis and suggestions for improvement should be fed back to the Research and PhD studies Committee (FUN) by the course coordinator.


If the course is withdrawn or is subject to major changes, examination according to this syllabus is normally offered at three occasions within/in close connection to the two following semesters.




Responsible for the course: Jörgen Adolfsson

Examiner: Jan-Ingvar Jönsson

Division of Microbiology and Molecular Medicine (MMM), Linköping University.

Course coordinator: Therese Pettersson

Sidansvarig: siw.carlfjord@liu.se
Senast uppdaterad: 2018-04-16