To become an independent user, user training is needed for the instrument of interest in the facility that the instrument is located in.

Before user training, it is good to get acquainted with basic flow cytometry (see end of the page). Remember to consider the experiment in hand (e.g. do you need to collect the cells of interest or just to analyse and how many or what kind of fluorocromes/markers/proteins will define intrument need). Contact personnel if you are planning a new experiment or have any questions. The training includes hands-on training for the instrument, usually one or two 2-3 h period with practical guidance for working in the facility and help with the first experiment set up. Remember then to schedule the first run with the personnel.

Training in Biomedicum

In Biomedicum you can get training for Analysers: Accuri C6 plus and Novocyte Quanteon or Sorters: Discover S8, BDAria II and Sony SH800s

Trainings are limited but you can request a training from iLab reservation system from "request services"-tab and we will get back to you for suggestions to schedule training time. You can register to the reservation system from the Fees and reservation system page.

Training in Viikki

In Viikki you can get training for the Analyser: BD LSRFortessa or the Sorters: BD FACSAria II and BD FACSAria Fusion.

Please contact the core personnel for more precise information on schedules. You can register to the reservation system from the Fees and reservation system page.

Marc Llort Asens

Introduction to Flow Cytometry Before User Training
Reservation and tips for sample prep


  • For service run, please make a request via "request service"-tab in iLab
  • After training you will get permission to reserve times yourself. Note that if you want the instrument to be on before you start, please make the reservation in a good time in advance. Short notice or out side office hours you might need to start the instrument yourself.
  • Please indicate information needed (if needed)
  • Cancellation for sorters is 24h and for analyzers 12h

Sample preparation

  • Only BSL1 cells; No infectious or pathogenic samples are allowed. All human samples from screened persons only. Transduced cells must be certified RCV negative. Bacterial and iPS samples must be discussed with personnel.
  • To remove debris and excess antibody, wash samples in PBS or FACS buffer.
  • Cell concentration depends quite a lot on your cells and experiment. With high efficiency and resolution experiments (e.g. Cell cycle, plate sorting and big or “sticky” cells) slower is better, 1 million/ml is usually a quite good concentration. With tube sorting for instance you can test 5-10 million/ml and have buffer on hand to dilute if needed.
  • Remember that there should be around 100ul dead volume in the sample (amount in the end that you should not run to prevent air going into the system)
  • If you use FACS buffer or PBS with low serum if any (max 2 % filtered). If necessary you can use medium but remember that high amount of serum and phenol red will give some fluorescence background.
  • With tissue culture you might need to optimize all the steps based on the tissue in question. Tissue samples tend to give lot of fluorescence background from cell debris. Consider using viability dye.


  • For set up, it is always advisable to have an unstained control sample and multicolor experiments will need all separately stained controls for compensation.
  • Multicolour experiments should be planned thoroughly to avoid unnecessary overspills and compensation spread; Small populations with brighter colours and subpopulations should not have spilling from previous population…

BD biosciences web page Panel design  

  • Remember to use Fc-blockers if needed/provided.
  • Always prefer primary antibodies if possible.
  • When fixing the samples please keep in mind the experiment in hand; What fixative do you need, do you need to study viability, staining first or after (intracellular or out, some antibodies might lose fluorescence), cells become buoyant so be careful with handling. Biorad Permeabilization and Fixation

Thermofisher Cell Preparation for Flow Cytometry Protocols


  • Always filter samples before sorting and remember to have tubes and buffer for the sort collection. You can pre-coat the inner walls of the collection tubes with a protein containing solution.
  • For collecting few events-1000 cells, use plate. For thousands, up to few hundred thousand you can use 1-2ml tubes. About million cells into 5ml tube and several millions into 15ml tube.
  • Consider using viability dye
  • Also consider sample temperature; if the cells are standing for long periods of time cooling the sample and instrument (sorters) to 4°C might be a good idea. Plate sorting or fast live analysis might be enough to have in RT.
Acknowledgment of the Flow Cytometry Unit

Please note that we expect you to acknowledge the Flow Cytometry Unit when publishing results using any of the instruments or services. e.g. “The flow cytometry analysis was performed at the HiLife Flow Cytometry Unit, University of Helsinki.” Kindly inform the personnel about your publication.