Table 1.
Markers used to identities cell cluster identities from scRNA-seq
| Cluster Number/Name | Cell Identity Markers | Top CIPR25, 26 match |
|---|---|---|
| 0 - Macrophages | Adgre1 | Interstitial macrophage (lung) |
| 1 - B cells (naïve) | Cd79a, Ms4a1, Ighd | Spleen follicular B cell |
| 2 - cDC2 (CD209) | Mgl2 | Adipose tissue CD11b− DC |
| 3 - Macrophages (Retnlahi) | Adgre | Interstitial macrophage (lung) |
| 4 - CD8+ T cells | Cd3d, Cd3g, Cd3e, CD8b1, Gzmk | Naïve CD8+ T cell 96 hours after in vitro stimulation |
| 5 - Monocytes | Ly6c2 | Blood Ly6C+ MHCII+ monocytes |
| 6 - B cells (activated) | Cd79a, Ms4a1, Ctla4, Mzb1 | Marginal zone B cell |
| 7 - NK cells | Gzma, Gzmb | Splenic NK cell Ly49H+ subset |
| 8 - cDC2 (Retnlahi) | Sirpa, Mgl2 | Adipose tissue CD11b+ DC |
| 9 - cDC1 | Flt3, Xcr1, Clec9a | Adipose tissue CD11b− DC |
| 10 - γδT cells | Tcrd, Tcrg, Tcre | Thymus B6 E15 TCRgammadelta |
| 11 - Proliferating cells | Mki67, Top2a, Ube2c | Pre-T cell double positive blasts* |
| 12 - ILC2 | Il2ra, Gata3, Arg163 | Innate lymphoid cells type 2 (intestine) |
| 13 - B cells (clonally expanded) | Cd79a, Ms4a1, Ighv1–58, Igkv6–15 | B cell (marginal zone) |
| 14 - Plasma cells | Jchain | Pre-T cell double positive all |
| 15 - CD4+ T cells | Cd3d, Cd3g, Cd3e, Cd4 | CD4+ T cell 8 days after LCMV infection |
| 16 - Migratory DCs | Flt3, Fscn1, Cacnb3, Nudt17, Socs264 | Skin draining lymph node DC |
| 17 - cDC2 | Flt3, Sirpa, Mgl2 | Thymus double negative DC |
| 18 - Macrophages (Cxcl13+) | Adgre1 | F4/80hi liver macrophage |
| 19 - Macrophages (peritoneal) | Adgre1 | Peritoneal macrophage steady state |
| 20 - pDC | Flt3, Pacsin1, Siglech, Irf8, Cox6a2, Runx264 | Spleen CD8- plasmacytoid DC |
*
Proliferating cells most closely matched Immgen cell types that are rapidly dividing due to the strong influence of cell cycle genes