How are single cells sorted in an scRNA-Seq protocol by FACS?
I will append the previous sentence in your protocol, and put what might help you in bold:


  To  obtain  B  cells,  NK  cells  and  monocytes,  a  splenocyte  suspension  was  stained  with PE-Cy7-conjugated  CD19,  eFluor  450-conjugated  NK-1.1,  PerCP  Cy5.5  Gr1,  FITC TCR-β,  APC  CD11b  and  PE  B220  (CD45R).  B220+ and  B220neg (germinal  center)  B cells  were  collected  by  gating  for  CD19+(TCR-βneg)  cells  and  then  by  B220  against  theCD19  marker.  NK  single  cells  were  collected  from  the  CD19neg/TCR-βneg events  by gating  for  NK-1.1  positive  events  in  NK-1.1  vs.  Gr1.


The cell types in question have unique properties that can be stained for using (immuno)histochemistry, i.e. chemicals and/or antibodies. The antibodies themselves tend to be conjugated, i.e. they are covalently bound to fluorophores typically which are fluorescent. That means a cell type can be labeled by fluorescence, and the FACS machine can sort fluorescent cells from non-fluorescent cells.

They stained the different cell types with different markers. The markers are sufficiently different from each other to be able to use them together in some cases. For instance, whatever FITC is could be used simultaneously with PE-Cy7-conjugated antibody.


First, they collect two subsets of B cells (the B220 positive and negative cells) by using the CD19 marker (PE-Cy7-conjugated antibody that binds CD19).
Then, from one of the subsets, the B220 positive one, they sort another subset which is positive for eFluor 450 (which is conjugated with an NK-1.1 antibody). This collected subset fulfills their criteria for being NK cells.
This subset is used for single cell capture on a plate (e.g. for SMART-seq2) or using microfluidics (e.g. for 10X Chromium).


For a FACS machine, you can select the threshold level of e.g. florescence that will be used as a cutoff between positive and negative events (cells). This is arbitrary and is usually subject to trials.