Fig. 2

Hypothetical example showing the pseudo-time ordering of cells collected from the root meristem. (upper) The green-colored cells represent a reporter marking the endodermis and quiescent center (QC). The color gradient represents a continuum of cellular maturation from birth (at bottom) to differentiation (towards the top). Cells are dissociated and isolated using fluorescence-activated cell sorting (FACS), whereupon ordering information is lost. At the right, single-cell expression profiles are used to infer a pseudo-ordering as cells in an approximate sequence. (lower) Two general methods of pseudo-time ordering are shown. Method 1 is unsupervised, using dimensionality reduction to position cells in a hypothetical space and then imposing an optimal path that infers the developmental progression of cells (e.g., Monocle). Method 2 uses markers to place cells in a specific location or developmental zone, with specific approaches differing in the way they adapt to false negatives and false positives. Seurat infers the expression of missing “gold-standard” markers based on coexpressed genes. Index of cell identity (ICI) employs many markers that “vote” on cell localization, where misleading diagnostic markers from false positives and false negatives are overcome by a majority of true positives. (Schematic by Ramin Rahni)