In our cell type atlas, we define Erythrocytes and Platelets, as well as 3 subtypes of Progenitor cells based on marker gene expression and cell types previously described in literature. Descriptions of the marker expression criteria are provided below.
The hierarchical relationships between types, the usage of labels at each level of our cell type hierarchy, and the number and proportion of cells relative to parent populations and the full dataset (All) are shown here:
| Cell Type | Level(s) | N cells | % of Parent | % of All |
|---|---|---|---|---|
| Erythrocyte | 1, 2, 3 | 1508 | NA | 0.08% |
| Platelet | 1, 2, 3 | 7903 | NA | 0.43% |
| Progenitor cell | 1, 2 | 1526 | NA | 0.08% |
| ├ CLP cell | 3 | 373 | 24.44% | 0.02% |
| ├ CMP cell | 3 | 1075 | 70.45% | 0.06% |
| └ BaEoMaP cell | 3 | 78 | 5.11% | 0.00% |
Cell type definitions
Level 1
At Level 1, we define the major classes in this category:
- Erythrocyte: Erythrocytes, often referred to as red blood cells, are cells that carry hemoglobin throughout the body. These cells can be identified by expression of the hemoglobin alpha 1 and 2 gene or the hemoglobin beta gene (HBA1, HBA2, and HBB, respectively). Erythrocytes also lack a nucleus, so have fewer detected genes per cell than most other cell types.
- Progenitor cell: Progenitor cells are rare in peripheral blood, and this class encapsulates three diverse progenitor cell types found in blood, which are described in more detail at Level 3. Progenitor cells can be identified by expression of the small integral membrane protein 24 gene (SMIM24) or the CD34 molecule gene (CD34).
- Platelet: Platelets are blood clotting components derived from the cytoplasm of megakaryocytes and lack a nucleus. They can be identified by high levels of the pro-platelet basic protein gene (PPBP) and the tubulin beta 1 class VI gene (TUBB1).
Level 2
At Level 2, we retain the cell classes used at Level 1.
Level 3
At Level 3 of our annotations, we divided the Progenitor cells based on expression of specific gene programs. Erythrocytes and Platelets were not divided further.
Progenitor cells cells were divided into 3 subpopulations:
- CLP cell: Common lymphoid progenitor (CLP) cells give rise to lymphoid cell types including T, B, and NK cells.
- CMP cell: Common myeloid progenitor (CMP) cells produce megakaryocytes and precursors to erythrocytes, monocytes, and granulocytes.
- BaEoMaP cell: Basophil, eosinophil, mast progenitor (BaEoMaP) cells are precursors derived from CMP cells that specialize in development of these granulocyte populations.
Marker visualizations
Key markers used to define NK and ILC cell types are shown in this figure, where we display a violin plot for each marker gene and each Level 3 cell type:
Expression of key marker genes shown on our UMAP projection:
