Fig. 3

Analysis of mass cytometry data to identify the hematopoietic differentiation hierarchy. a Known hematopoietic hierarchy in the healthy human bone marrow. Hematopoietic stem cells (HSCs) are at the apex of the hematopoietic hierarchy and can produce progenitor cells, such as multipotent progenitors (MPPs), common myeloid progenitors (CMPs) and common lymphoid progenitors (CLPs). CLPs can give rise to T-lineage cells and B-lineage cells. CMPs can differentiate into either megakaryocyte-erythroid progenitors (MEPs) or granulocyte–macrophage progenitors (GMPs). MEPs can further differentiate into megakaryocytes and erythrocytes, whereas GMPs will become monocytes and granulocytes. b Workflow of constructing the tree-shaped trajectory using the 13-panel mass cytometry data. Raw FCS files were read using CytoTree. SOM clustering was performed using all cells. The cells were downsampled in a cluster-dependent fashion. The clusters of all cells were linked by MST to illustrate the differentiation relationship based on the n-dimensional hull after dimensionality reduction. c Tree plot with putative cell subpopulations annotated manually in yellow circles. The tree plot was constructed using 13 cell surface antigens present in healthy human bone marrow and revealed the hematopoietic differentiation lineages. The color of each cluster represents the branches identified. d Expression markers of CD4, CD8, CD11b, CD19, CD20, CD33, CD34, CD38, CD45, CD45RA, and CD123 expression markers are overlaid on the tree plot. The expression levels of the markers in each cluster were calculated by SOM clustering. These markers were used for the clustering to help define the different cell lineages