Mike Barnkob:Protocols/Immunology/Flow/General notes

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General notes on flow cytometry

Antibody selection

• Selection bright fluorochrome (PE, brilliant violet, 488) for markers that are less expressed, and less-bright ones for markers that are highly expressed
• Auto-fluorescence is higher in lower light-ranges

Isotype controls

• Use same species and IgG-isotype, with same fluorochrome is possible (meaning buying from same company as other antibody).
• Age affects fluorochrome
• Use at same concentration as target
• Unspecific binding: IgG1 < IgG2 < IgM

Tamdem dyes

• Are affect more by temperature. Stain at 4c, not on ice. Also don’t keep in back of fridge, where it might be colder.
• De-conjugates more after dilution

Compensation

• Beads are good, but: don’t account for fluorochrome changes and auto-fluorescence. Beads are best for T-cells, but work badly for many other cell types.
• Brilliant violet dyes are very hard to compensate, since they react with each other
• Tandem-dyes may uncouple
• During voltage changes – remember to check not only channel compensating, but also other channels which the color bleeds into.
• When seeing big data spread, consider 1) lowering voltage, 2) change antibody.

Doublet exclusion

• Be especially carefully when doing CFSE staining, here it is better to take all.
• If set to stringently, will exclude cells that are dividing and of interest.
• FSC-A / FSC-W is better SSC-A/SSC-W.
• Consider doublet discrimination in the end, instead of after FSC-SSC

Sorting

• Don’t use phenol red, increases auto-fluorescence
• Filter solution
• Wash at lower velocity (150g for 5 min)
• Sort into media
• Slowly shake the collection tube often, because cells will splash against walls of tubes and die if they don’t get into media