Fig. 8

The manual gating strategy applied for cell-type annotation in PBMC-1, using its surface marker expression data. In general, we follow the gating strategy outlined in Maecker et al. [19]. We first gate GEMs on CD3 and CD19. CD3⁺ GEMs are further gated over CD4 and CD8. CD3^-CD19^- GEMs are further gated over CD14 and CD56. For GEM clusters gated from the CD14-CD56 penal, the CD14⁺ and CD56⁺ GEMs are further gated over CD16. The CD14^-CD56^- GEMs are gated over CD11c to extract CD11c⁺ DC GEMs. The 8 cell types commonly observed in PBMCs are highlighted in green bounding boxes. Some GEM clusters, such as the CD3⁺CD4⁺ GEM cluster, go through additional gating, in order to reveal non-conventional sub-clusters in PBMCs (which are later classified as phony-type GEM clusters), such as the CD3⁺CD4⁺CD14⁺ GEM cluster or the CD3⁺CD4⁺CD56⁺ GEM cluster. Non-conventional GEM clusters are highlighted in orange bounding boxes