Extended Data Table 7.
Definitions of each cell subset in flow cytometry with specific markers.
| Cell population | Definition by markers | |
|---|---|---|
| Flow cytometry staining panels | Live singlet gate | PBMC/Single Cells/Single Cells/Live... |
| 1: PBMC cell composition staining | B cells | .../CD19+CD3- |
| T cells | .../CD19-CD3+ | |
| NKT cells | .../CD19-CD3+/CD3+CD56+ | |
| NK cells | .../CD19-CD3-/CD56+CD66b- | |
| Classical Monocytes (cMono) | .../CD19-CD3-/CD56-CD66b-/CD14+CD16- | |
| Intermediate Monocytes (intMono) | .../CD19-CD3-/CD56-CD66b-/CD14+CD16var | |
| Non-Classical Monocytes (ncMono) | .../CD19-CD3-/CD56-CD66b-/CD14-CD16+ | |
| Plasmacytoid DCs (pDC) | .../CD19-CD3-/CD56-CD66b-/CD14-CD16-/CD304+ | |
| Macrophages | .../CD19-CD3-/CD56-CD66b-/CD14-CD16-/CD304-/CD11b+ | |
| DC1 | .../CD19-CD3-/CD56-CD66b-/CD14-CD16-/CD304-/CD141+HLA-DR+ | |
| DC2 | .../CD19-CD3-/CD56-CD66b-/CD14-CD16-/CD304-/CD1c+HLA-DR+ | |
| 2: T cell subsets staining (by surface markers) | CD8 T cells | .../CD3+/CD8+CD4- |
| Naïve CD8T | .../CD3+/CD8+CD4-/CD3+CD45RA+/CD127+CCR7+/CD3+PD1- | |
| Temra CD8T | .../CD3+/CD8+CD4-/CD3+CD45RA+/CD127-CCR7- | |
| Central Memory CD8T (CD8Tcm) | .../CD3+/CD8+CD4-/CD3+CD45RA-/CD127+CCR7+ | |
| Effector Memory CD8T (CD8Tem) | .../CD3+/CD8+CD4-/CD3+CD45RA-/CD127+CCR7- | |
| Terminally Differentiated CD8T (PD-1+TIM-3+CD8) | .../CD3+/CD8+CD4-/CD3+CD45RA-/TIM3+PD1+ | |
| Follicular CD8T (FoIICD8) | .../CD3+/CD8+CD4-/CD3+CD45RA-/CXCR5+PD1+ | |
| TCR-activated CD8T (CD38+HLA-DR+CD8) | .../CD3+/CD8+CD4-/CD38+HLA-DR+ | |
| CD4 T cells | .../CD3+/CD8-CD4+ | |
| Naïve CD4T | .../CD3+/CD8-CD4+/CD3+CD45RA+/CD127+CCR7+/CD3+PD1- | |
| Temra CD4T | .../CD3+/CD8-CD4+/CD3+CD45RA+/CD127-CCR7- | |
| Resting Natural Regulatory CD4T (CD4rn Treg) | .../CD3+/CD8-CD4+/CD3+CD45RA+/CD127-CD25hi/CD3+HLA-DR- | |
| Central Memory CD4T (CD4Tcm) | .../CD3+/CD8-CD4+/CD3+CD45RA-/CD127+CCR7+ | |
| Effector Memory CD4T (CD4Tem) | .../CD3+/CD8-CD4+/CD3+CD45RA-/CD127+CCR7- | |
| Terminally Differentiated CD4T (PD-1+TIM-3+CD4) | .../CD3+/CD8-CD4+/CD3+CD45RA-/TIM3+PD1+ | |
| Effector Regulatory CD4T (CD4effTreg) | .../CD3+/CD8-CD4+/CD3+CD45RA-/CD127-CD25hiTreg/CD3+HLA-DR+ | |
| Natural Regulatory CD4T (CD4n Treg) | .../CD3+/CD8-CD4+/CD3+CD45RA-/CD127-CD25hiTreg/CD3+HLA-DR- | |
| TCR-activated CD4T (CD38+HLA-DR+CD4) | .../CD3+/CD8-CD4+/CD38+HLA-DR+ | |
| 3: Cytokine producing T cells staining (intracellular staining) | Granzyme B-expressing CD8T | .../CD3+/CD8+CD4-/GranzymeB+ |
| IFNy- expressing CD8T | .../CD3+/CD8+CD4-/IFNy+ | |
| TNFa-expressing CD8T | .../CD3+/CD8+CD4-/TNFa+ | |
| IL2- expressing CD8T | .../CD3+/CD8+CD4-/IL2+ | |
| IL6-expressing CD8T | .../CD3+/CD8+CD4-/IL6+ | |
| CXCR3-expressing CD8T | .../CD3+/CD8+CD4-/CXCR3+ | |
| IFNy- expressing CD4T | .../CD3+/CD8-CD4+/IFNy+ | |
| TNFa-expressing CD4T | .../CD3+/CD8-CD4+/TNFa+ | |
| IL2- expressing CD4T | .../CD3+/CD8-CD4+/IL2+ | |
| IL6-expressing CD4T | .../CD3+/CD8-CD4+/IL6+ | |
| IL4-expressing CD4T | .../CD3+/CD8-CD4+/IL4+ | |
| IL17-expressing CD4T | .../CD3+/CD8-CD4+/IL17+ | |
| CXCR3-expressing CD4T | .../CD3+/CD8-CD4+/CD3+CXCR3+ | |