Figure 3.

Marker gene–based identification of cell clusters.A, expression of cell type–specific marker genes was used to annotate individual cell clusters. Log2 expression intensity values of individual cells are indicated (color scale). B, the Col2a1⁺ main population was identified, and subpopulations of articular (Cre—green, CreTW—orange), prehypertrophic/hypertrophic (Cre—purple, CreTW—red), and unique chondrocytes (Cre—pink, CreTW—brown) are highlighted. Cells with low UMI counts and noncartilaginous cells were excluded from the analysis. C, cluster-specific cell numbers within the Col2a1⁺ main subpopulation of Cre and CreTW mice are shown in split t-SNE plots. t-SNE, t-distributed stochastic neighbor embedding; UMI, unique molecular identifier.