BD FACSAria II cell sorter 

Access: with an Operator or training required (3-4 experimental sessions)

General Description 

BD FACSAria II is a high-speed fixed alignment benchtop cell sorter. It uses three low-powered lasers: violet (407nm, 30mW), blue (488nm, 13mW) and red (633nm, 11mW). The system is equipped with forward (FSC) and side (SSC) scatter detectors and 9 fluorescence detectors: 

  • violet 407 (530/30, 450/50) 

  • blue 488 (780/60, 695/40, 616/23, 585/42, 530/30) 

  • red 633 (780/60, 660/20).  

The tube holders for 1 ml1.5 mlml and 15 ml are provided. BD FACSAria II can sort up to four populations simultaneously. The variety of particle sizes can be accommodated thanks to integrated nozzles available in four sizes (70 µm, 85 µm, 100 µm & 130 µm). There is no multi-well plate sorting module. 

Sample preparation 

  • Prepare cells suspension in filtered buffer (PBS with 2% BSA + 2.5 mM EDTA) but if necessary, in any other medium without phenol red and FCS. 

  • The sample should have particles density of approximately 5-10 million/ml. If less cells are available put then into minimal volume of 500 µl. 

  • Negative controls and individual positive controls of your staining are required to set sorting gates appropriately. 


  • To improve cells viability, make all preparation steps on ice, unless otherwise stated in your protocol.  

  • To exclude dead cells from the analysis or sorting it is recommended to use DNA-binding dyes as a marker of dead cells.  

  • DNA released from dead cells during cells dissociation causes stickiness. To reduce cells aggregation in your samples, incubate the cells in the presence of DNase I (100 ug/ml with 5 mM MgCl2). 

Further Reading 

  • BD_FACSAria_II_User_Guide 
  • Quick FACSAria turn on 
  • BD_FACSAriaII IIMCB configurations 
  • 2019 Guidelines for the use of flow cytometry and cell sorting in immunological studies_second edition 
  • DIVA software 6.0